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5 Best Pharmacy POS Systems

Ideally, a pharmacy POS should include HSA and FSA payment acceptance and should also integrate with your medical billing and pharmacy management systems.

    Kymberlin Bush
  • Last updated onUpdated

  • Matt Sherman
  • REVIEWED BY

    Matt Sherman

    Lead Staff Writer

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The best POS systems for small businesses process payments and manage your inventory, employees, and customers.

The best POS systems for pharmacies will also include specific features like HSA/FSA payment acceptance, medical billing and pharmacy management system integrations, and even online ordering or prescription delivery.

Learn More About Our Top Picks

CompanyBest ForNext StepsBest For
Lightspeed Retail

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  • Best for advanced retail features
  • Offers local delivery, advanced inventory management, and robust vendor/supply chain management tools
  • Pricing starts at $69/month
  • Best for advanced retail features
  • Offers local delivery, advanced inventory management, and robust vendor/supply chain management tools
  • Pricing starts at $69/month

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Shopify POS

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  • Best for in-person and online orders
  • Easy-to-make online store, FSA/HSA acceptance, and multichannel inventory syncing
  • Pricing starts at $29/month
  • Best for in-person and online orders
  • Easy-to-make online store, FSA/HSA acceptance, and multichannel inventory syncing
  • Pricing starts at $29/month

Visit Site

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Square POS

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  • Best Free Pharmacy POS
  • Offers FSA/HSA acceptance, integrates with EHR and medical billing software, free POS app and website
  • Pricing starts at $0/month
  • Best Free Pharmacy POS
  • Offers FSA/HSA acceptance, integrates with EHR and medical billing software, free POS app and website
  • Pricing starts at $0/month

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Cashier Live

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  • Best for pharmacy software integrations
  • Offers a dedicated pricing plan for pharmacies, FSA card acceptance, and pharmacy management integration
  • Pricing starts at $75/month
  • Best for pharmacy software integrations
  • Offers a dedicated pricing plan for pharmacies, FSA card acceptance, and pharmacy management integration
  • Pricing starts at $75/month

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Clover POS

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  • Best for ease of use
  • Offers a plug-and-play POS system, FSA/HSA acceptance, and healthcare payment processor integrations
  • Pricing starts at $0/month
  • Best for ease of use
  • Offers a plug-and-play POS system, FSA/HSA acceptance, and healthcare payment processor integrations
  • Pricing starts at $0/month

Visit Site

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Show Fewer Options

Read more below to learn why we chose these options.

Top Pharmacy POS Software

Features like multi-store support, customer loyalty programs, reporting, and inventory/delivery management make some POS systems stand out as great choices for pharmacies. Our top picks include:

How The Best Pharmacy POS Systems Compare

Multi-Store Support Loyalty Program Inventory Management Reporting Delivery Management
Lightspeed Retail Advanced plan & up Third-party integration
Shopify POS Multiple inventory locations Third-party integration
Square Paid add-on Third-party integration
Cashier Live
Clover

Lightspeed Retail: Best Advanced Retail Features

Lightspeed Retail

Total Rating 4.1
Pricing3.7

Ease Of Use4.4

Features4.3

Customer Service4.1

User Reviews4.0

Pricing

$89-$269/month ($69-$199/month billed annually)

Contract

Monthly, annual, and custom

Equipment Cost

$199-$329

Pros

  • Third-party delivery app integrations for local Rx delivery
  • Advanced inventory tracking and reporting
  • Vendor and supply chain management tools

Cons

  • It can get expensive if you want all the options
  • No out-of-the-box pharmacy software integrations
  • Early termination fee

Why We Chose Lightspeed For Advanced Retail Features

We love Lightspeed Retail's advanced features for business owners who need something a little more than a basic POS system can provide.

Lightspeed Retail offers advanced inventory management, vendor management, and supply chain management tools for busy pharmacies.

Lightspeed Retail Pricing

Lightspeed Retail Plans Price  When To Use
Lean Plan $89/month ($69/month billed annually) For single/multi-location retail business looking for strong inventory management and a customizable POS interface
Standard Plan $149/month ($119/month billed annually) For single/multi-location retail businesses looking for eCommerce and accounting features
Advanced Plan $269/month ($199/month billed annually) For single/multi-location retail businesses looking for a strong loyalty program and advanced business reporting

Pricing ranges from $89 to $269/month ($69/month to $199/month with annual billing). Lightspeed also has quote-based enterprise pricing for large businesses.

All plans come with one POS register. To add extra registers, you’ll pay $59/register/month.

Lightspeed Retail Features

Lightspeed Retail Features Availability
Multi-Store Support
Contactless Payments
Multi-Channel Selling Standard plan and up
Gift Cards
Customer Loyalty Advanced plan
Marketing Tools Standard plan and up
Online Ordering Standard plan and up
Inventory Management
Reporting
Menu Management
Delivery Management
EBT Acceptance
Employee Management
Text Messaging

Lightspeed is one of the best retail POS systems. It is especially well-suited for retail establishments processing large amounts of transactions every day, like a pharmacy.

This is because Lightspeed is the leader as one of the best POS systems for inventory management. This pharmacy POS harnesses the power of the cloud to provide advanced retail features, including inventory management, vendor management, customer management, loyalty, accounting, and eCommerce.

Lightspeed is as flexible as it is powerful; its open API allows you to build your own third-party pharmacy software integrations to customize your perfect pharmacy POS.

Hardware Costs

Lightspeed’s POS hardware is iPad-based, and you’ll have to contact the company for a personalized quote. You can also source your hardware yourself.

Note: Lightspeed Retail now requires all new and existing qualified merchants using Lightspeed Retail in the US and Canada to sign up for Lightspeed Payments, Lightspeed’s payment processor. If you currently use a card reader from a third-party payment processor, you can’t use it anymore. Since you can’t use any existing payment terminals (card readers) with Lightspeed Payments, Lightspeed is currently running a free terminal replacement promotion for eligible merchants that includes two free Lightspeed POS terminals (card readers) per qualified merchant.

Eligible merchants include business owners that process a minimum of $100/day in credit card payments, as measured by a monthly average. Apple products are not included in this promotion, so you’ll still need to source an iPad to take sales.

Lightspeed Retail Payment Processing

Lightspeed provides flat-rate payment processing via Lightspeed Payments at a rate of 2.6% + $0.10.

Note: Lightspeed will buy out payment processing contracts, paying off merchants’ early cancellation fees if you process a minimum of $25,000 in card sales and then submit documentation of your previous payment processing contract that states your early termination fee within six months of meeting this minimum processing amount.

It’s important to note that the “paying off” comes in the form of discounted payment processing fees, not a chunk of cash that goes towards your termination fees when you decide to switch to Lightspeed Payments.

If you are a current Lightspeed user and don’t apply for Lightspeed Payments within 30 days of receiving a notification email, you’ll be charged a fee between $200 and $1,120 per month until you do sign up for Lightspeed Payments.

What To Watch Out For

To get the best pricing for Lightspeed, you’ll need to prepay for one year. However, we often advise readers to sign up for short-term monthly plans before dedicating themselves to the long term. This is because many POS providers (Lightspeed included) charge an early termination fee for canceling a plan early.

You also need to use Lightspeed Payments to get the best monthly subscription rate. If you use a different integrated payment processor, you will pay an extra $50/month to do so. This extra fee may be worth it for larger businesses that can offer better payment processing rates than Lightspeed.

If you purchase hardware from Lightspeed, you must confirm that you have received it within five business days. Otherwise, your hardware will not be covered under Lightspeed’s hardware warranty (14 days for Apple products and 30 days for non-Apple products).

Lightspeed Retail Is Best For Pharmacies That:

  • Need advanced retail reporting, inventory tracking, and employee management
  • Want to offer local delivery
  • Want a POS system with an open API

Get Started With Lightspeed Retail

Read our in-depth review

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Shopify POS: Best For In-Person & Online Orders

Total Rating 4.3
Pricing4.0

Ease Of Use4.9

Features4.4

Customer Service4.8

User Reviews4.4

Pricing

Starts at $29/month

Contract

None

Equipment Cost

$0-$500+

Pros

  • Easy-to-add online store
  • FSA/HSA payment acceptance
  • Multichannel inventory syncing

Cons

  • Limited offline mode
  • No dedicated merchant account

Why We Chose Shopify POS As The Best For In-Person & Online Orders

We love the eCommerce options Shopify offers users, and Shopify POS increases the feature set by adding in-person sales.

Pharmacies can expect an easy-to-use (and design) online store, FSA/HSA payment acceptance, and multichannel inventory syncing from Shopify POS.

Shopify Pricing

Shopify POS Plans Price  When To Use
Basic $39/month ($29/month billed annually) If you have a growing eCommerce business with occasional in-person sales
Shopify $105/month ($79/month billed annually) If you want additional reporting and reduced payment processing fees
Advanced $399/month ($299/month billed annually) If you want advanced reporting and additional discounts on processing fees
Shopify Plus $2,000+/month If your high-volume or large business needs an enterprise-level solution

Pricing for a basic Shopify POS + Shopify website ranges from $29 to $299/month (billed monthly) with unlimited devices on all plans. To add the full suite of POS features, including advanced inventory, you’ll need to add Shopify Pro, which is an additional $89/month. Shopify also offers a Shopify Starter plan ($5/month) for mobile processing only and Shopify Plus plans for enterprise-level businesses.

Shopify Features

Shopify POS Features Availability
Multi-Store Support Supports multiple inventory locations
Contactless Payments
Multi-Channel Selling
Gift Cards
Customer Loyalty
Marketing Tools
Online Ordering
Inventory Management
Reporting
Menu Management
Delivery Management
EBT Acceptance
Employee Management
Text Messaging

Shopify is a complete commerce solution for both online and brick-and-mortar businesses. However, Shopify especially shines in terms of its eCommerce features. If you work with a developer, there’s nothing you can’t do with a Shopify website. Notably, Shopify Plus powers multiple enterprise-level online pharmacies, including Meagher’s Pharmacy and Lloyd’s Pharmacy.

Even for a smaller pharmacy, Shopify has numerous eComm integrations that can be useful for pharmacies that want to sell in-person and online, including SnapRx, Retail Management Solutions, and various age verification apps.

Hardware Costs

Shopify sells hardware bundles and individual hardware components; you can also source your iPad or Android POS hardware yourself. Shopify’s most affordable bundle, which includes a stand for a 9.7″ iPad and a card reader, is priced at $219.

Shopify Payment Processing

Shopify has an in-house payment processing service called Shopify Payments, which is powered by Stripe. Rates range from 2.3% to 2.7%, depending on which Shopify plan you’re on. You can also integrate a payment processor of your choice for an additional transaction fee.

What To Watch Out For

All Shopify plans are month-to-month with no long-term commitment required. Note that Shopify Payments is a payment service provider similar to Square or PayPal, which means you will not have your own dedicated merchant account.

Shopify POS Is Best For Pharmacies That:

  • Want to sell both online and in-person
  • Don’t need a dedicated merchant account
  • Aren’t worried about limited offline capabilities

Get Started With Shopify POS

Read our in-depth review

Jump back to comparison chart

Square POS: Best Budget-Friendly Option

Total Rating 4.9
Pricing4.9

Ease Of Use5.0

Features4.8

Customer Service4.7

User Reviews4.8

Pricing

$0/month

Contract

None

Equipment Cost

$49-$799

Get a free card swiper from Square at no cost when you create a free account. Claim your card reader.

Pros

  • Accepts FSA/HSA cards
  • Integrates with EHR and medical billing software
  • Free POS app & website

Cons

  • Must use Square for payment processing

Why We Chose Square As The Most Budget-Friendly Pharmacy POS

Need a low-risk, low-commitment, low-cost POS system? Square is the first place you should probably look no matter what kind of business you own.

We love the robust features available to pharmacies at little to no cost including FSA/HSA acceptance, EHR and medical billing software integrations, and Square's great free POS app and website.

Square Pricing

Square POS Plans Price  When To Use
Free Plan $0/month If you have basic POS and processing needs
Square Appointments $0-$69/month If you are a business with extensive scheduling needs
Square For Retail $0-$89/month If you are a retail business with needs for advanced features
Square For Restaurants $0-$60/month If you are in the foodservice industry and need restaurant-specific features
Square Online Store $0/month depending on plan If you have eCommerce needs

Square POS has no monthly fee. Square also offers two versions of Square for Retail if you want advanced inventory features, including a free and paid ($60/month) version.

Square Features

Square POS Features Availability
Multi-Store Support
Contactless Payments
Multi-Channel Selling
Gift Cards Add-on
Customer Loyalty Add-on
Marketing Tools
Online Ordering
Inventory Management
Reporting
Menu Management With Square for Restaurants
Delivery Management Add on
EBT Acceptance
Employee Management
Text Messaging

For a free POS app, Square offers a ton of functionality.

Not only is Square perfect for basic, easy-to-use payment processing, but this free POS also has a ton of extensions and app integrations that extend its functionality for any business type, including healthcare businesses such as pharmacies. Some examples include DrChrono EHR & RCM, Remedly, IntakeQ, and Reference Health Payments.

Square also includes FSA and HSA payment acceptance out-of-the-box as long as you have an eligible MCC (merchant category code). Even enterprise-level companies such as QuigMeds have integrated Square technology into their pharmacy POS systems.

Hardware Costs

Square sells POS hardware for iPad as well as its proprietary Square Register ($799) and Square Terminal ($299); you can also source your POS hardware yourself. Square accounts come with a free card swiper, though most pharmacies will want a more secure $49 chip and tap reader, which you can use with an iPad or Android tablet.

Square Payment Processing

Square charges a flat rate of 2.6% + $0.10 for all in-person transactions. Square also offers custom pricing for enterprise businesses that process over $250K/month. You do not have the option to use a different payment processor with Square.

What To Watch Out For

All Square plans are month-to-month with no long-term commitment required. Square is a third-party payment processor/payment service provider rather than a merchant account provider, which can result in account stability problems for certain businesses.

Square Is Best For Pharmacies That:

  • Want an affordable or free and comprehensive POS system
  • Need EHR and medical billing software integration
  • Want a free POS app and website for online sales

Get Started With Square POS

Read our in-depth review

Jump back to comparison chart

Cashier Live: Best Software Integrations

Cashier Live


Visit Site


Pros

  • Dedicated plan for pharmacies
  • SIGIS-certified system to accept FSA cards
  • Pharmacy management integration
  • Prescription wholesaler purchase ordering

Cons

  • Limited offline mode
  • Expensive hardware

Why We Chose Cashier Live For The Best Pharmacy Software Integrations

Cashier Live offers something the other POS systems on this list don't: a dedicated pharmacy plan.

Their dedication to this industry allows them to offer important pharmacy software integrations like SpeedScript, HBS, Carepoint, RNA, and MethCheck (for pseudoephedrine sales).

Cashier Live Pricing

Cashier Live’s pharmacy plan pricing is quote-based. However, the company says its software provides the best value in the industry, with no hidden fees. Though Cashier Live doesn’t list its pharmacy plan pricing, the company’s standard retail package is $75/month, which is quite reasonable.

Cashier Live Features

Cashier Live Features Availability
Multi-Store Support Unknown
Contactless Payments Unknown
Multi-Channel Selling Unknown
Gift Cards Unknown
Customer Loyalty Unknown
Marketing Tools Unknown
Online Ordering Unknown
Inventory Management Unknown
Reporting Unknown
Menu Management Unknown
Delivery Management Unknown
EBT Acceptance Unknown
Employee Management Unknown
Text Messaging Unknown

The main benefit of using Cashier Live is that it has pharmacy POS features out of the box, including built-in integrations with other pharmacy software systems. In fact, Cashier Live was the first web-based SIGIS (Special Interest Group for IIAS Standards)-compliant POS system built for pharmacy needs.

Other pharmacy-specific POS systems tend to be locally-installed and exorbitantly expensive, so Cashier Live is a great cloud-based alternative. Some industry-specific integrations included with Cashier Live are SpeedScript, HBS, Carepoint, RNA, and MethCheck (for pseudoephedrine sales).

Hardware Costs

Cashier Live can run on iOS, Android, or a computer, which gives you the option to source hardware components yourself. However, the company’s hardware bundles are on the expensive side. For example, Cashier Live PayPoint POS hardware for pharmacies goes for $2,599.

Cashier Live Payment Processing

Cashier Live offers a flat rate of 2.7% on each transaction. The POS company does not integrate with other processors.

What To Watch Out For

Cashier Live contracts are billed month-to-month with no long-term contract required. However, you can receive a discount if you commit to a year or more.

Cashier Live Is Best For Pharmacies That:

  • Have important existing pharmacy software integrations
  • Need a pharmacy management integration
  • Want prescription wholesaler purchase ordering features

Get Started With Cashier Live

Jump back to comparison chart

Clover POS: Best For Ease Of Use

Total Rating 4.3
Pricing4.0

Ease Of Use4.8

Features4.5

Customer Service4.4

User Reviews4.1

Pricing

Starts at $0/month

Contract

Depends on merchant services provider

Equipment Cost

$49-$1,799 per device

Pros

  • Plug-and-play POS system
  • FSA/HSA acceptance
  • Healthcare-friendly payment processors integrations

Cons

  • Proprietary hardware can’t be used with other systems
  • Sold by some low-quality resellers

Why We Think Clover Is The Easiest To Use

Clover is hand-down one of the best plug-and-play POS systems on the market.

Pharmacies looking for a POS system that is quick to learn, train, and troubleshoot could do much worse than Clover. While it isn't a pharmacy-specific POS, there are plenty of third-party integrations you can use to make Clover a great POS for you.

Clover Pricing

Clover POS Plans Price  When To Use
Clover Payments $0/month If you only need to process payments and don’t need any POS hardware
Clover Essentials $14.95/month If you have a small retail/service-based business and don’t take returns
Clover Register $49.95/month If you have a small to mid-size retail/service-based business and need more POS features
Clover Counter Service Restaurant $54.95/month If you have a quick-serve restaurant, cafeteria, or mobile food service business
Clover Table Service Restaurant $84.95/month If you have a full-service restaurant or bar

Clover’s Register Plan (for any business type) starts at $44.95/month for one terminal if you purchase your equipment upfront. You can also opt to lease your equipment and receive the Register plan starting at $90/month. Clover also has an option that includes a virtual terminal to key in credit card payments online for $14.95/month.

Clover Features

Clover POS Features Availability
Multi-Store Support
Contactless Payments Depends on hardware choice
Multi-Channel Selling
Gift Cards
Customer Loyalty
Marketing Tools
Online Ordering Depends on software plan
Inventory Management
Reporting
Menu Management
Delivery Management
EBT Acceptance Add-on app
Employee Management
Text Messaging

Clover is an incredibly easy-to-use system that’s a breeze to set up and train your employees on. Pretty much as soon as you receive your POS hardware, you can plug it in, activate it, and start taking payments.

It’s a good system for basic payment acceptance if you don’t need a lot of pharmacy-specific features — although its REST API means you can integrate other REST-ful applications. Clover is not IIAS-compliant (which is required to accept HSA/FSA payments as a non-medical retailer), but as long as you have an eligible MCC code (MCC 5912 or 5122 for pharmacies), you can accept HSA and FSA cards with Clover.

Hardware Costs

Clover’s flagship Clover Station POS is $1,349. If you want a customer-facing screen, you can upgrade to the $1,799 Clover Station Duo. Other hardware options include the $799 Clover Mini and the mobile $499 Clover Flex.

Clover Live Payment Processing

If you purchase your system directly from Clover, payment processing fees range from 2.3% to 2.6%+ $0.10, depending on your monthly software plan. Various other entities also sell Clover with different (and often more expensive) payment processing structures.

What To Watch Out For

Hundreds of different merchant service providers sell Clover, and not all of them are top-notch. While software purchased from Clover directly is all month-to-month with the ability to cancel at any time, other providers may sell Clover with sneaky long-term contracts and hidden fees.

Clover Is Best For Pharmacies That:

  • Need a plug-and-play POS system
  • Want to choose a healthcare-friendly payment processor
  • Don’t mind proprietary hardware

Get Started With Clover POS

Read our in-depth review

Jump back to comparison chart

Methodology

Merchant Maverick has been researching and reviewing POS providers since 2012. Our writers have tested over 100 different point of sale systems, evaluating pricing, features, ease of use, customer service, and user reviewers. Read more about how we rate POS providers.

When comparing different POS software systems, we consider many data points, including relative pricing, the depth of niche features offered, the price of hardware, and any associated payment processing fees. Our lists of the best providers include only apps we’ve deemed worthwhile from multiple vantage points. The POS vendors we pick share qualities such as widespread availability, accessibility, user-friendliness, and reasonable pricing. We also look carefully at niche features, such as check-splitting, inventory management, eCommerce, loyalty programs, gift cards, and more.

We spend an average of 10-15 hours researching and updating each one of our lists, making sure the providers included meet our internal standards for quality and reputation.

80+

Vendors evaluated

65+

Attributes assessed per vendor

20+

Features weighed

30+

Combined years of experience


Finding The Best Pharmacy Point Of Sale System

When it comes to choosing among the above pharmacy pos systems it’s important to verify that the POS does everything you need it to. This is especially necessary for a highly regulated industry such as the pharmacy industry.

For example, you may need an IIAS-compliant system to accept FSA or HSA cards (the IRS requires this if less than 90% of your gross sales are from prescriptions and over-the-counter qualifying healthcare products). Or, if you run an online-only pharmacy that fulfills prescriptions based on telephone consults, you’ll likely need a high-risk merchant account.

Additionally, you will need to determine if a POS can integrate with your insurance billing and pharmacy management systems.

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Kymberlin Bush

Kymberlin Bush

Staff Writer
Kymberlin started contributing to Merchant Maverick as a freelancer in 2022 and joined the team as the full-time small business health insurance expert in 2023. She earned her Bachelor of Arts in Creative Writing from Pacific University in 2020 and continues to reside in Portland, Oregon.
Kymberlin Bush
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