5 Best Pharmacy POS Systems

Lightspeed also has quote-based enterprise pricing for large businesses.

All plans come with one POS register. Extra registers can be added for an additional monthly fee.

Lightspeed Retail is one of the best retail POS systems for pharmacies that process high volumes of transactions each day. It combines flexibility with advanced functionality, making it ideal for managing complex operations.

Key features include:

• Advanced Inventory Management: Track thousands of SKUs, automate reordering, and manage stock across multiple locations.
• Vendor Management: Simplify purchasing and supply chain tracking with integrated vendor catalogs and purchase orders.
• Customer Management: Store customer profiles, purchase history, and loyalty details for faster service and better insights.
• Built-In Accounting & Reporting: Generate detailed reports and sync seamlessly with accounting tools.
• eCommerce & Loyalty Tools: Sell online and reward repeat customers with built-in loyalty programs.
• Open API: Customize your setup or integrate with pharmacy management and billing systems for a seamless workflow.

Lightspeed’s POS runs on iPads, and you can either purchase hardware directly from the company or source it yourself.

All new and existing US and Canadian merchants must now use Lightspeed Payments, meaning third-party card readers are no longer supported. However, eligible merchants processing at least $100/day in credit card sales can receive two free Lightspeed POS terminals through the company’s replacement promotion. (Apple products like iPads are not included.)

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.

To get the best Lightspeed pricing, you’ll need to prepay annually, but we recommend starting with a monthly plan since canceling early can trigger termination fees.

You’ll also need to confirm receipt of any Lightspeed hardware within five business days to activate your warranty (14 days for Apple products, 30 days for non-Apple).

Unlimited devices are supported on all plans. To add the full suite of POS features, including advanced inventory, you’ll need to add Shopify Pro, which costs an additional monthly fee.

Shopify is a complete commerce platform that combines powerful online and in-person sales tools. While it works well for any retail business, it truly excels when it comes to eCommerce.

Key Shopify POS features for pharmacies include:

• Advanced eCommerce Tools: Build a custom online pharmacy storefront with professional templates and developer-friendly flexibility.
• Enterprise Scalability: Shopify Plus supports major online pharmacies like Meagher’s and Lloyd’s, proving its ability to handle complex retail operations.
• Pharmacy Integrations: Access useful apps such as SnapRx, Retail Management Solutions, and age verification tools to stay compliant and efficient.
• Omnichannel Syncing: Keep your in-store and online inventory, pricing, and customer data fully connected.

Shopify sells hardware bundles and individual hardware components; you can also source your iPad or Android POS hardware yourself.

Shopify has an in-house payment processing service called Shopify Payments, which is powered by Stripe. Rates are 2.4% – 2.7%  and are based on which Shopify plan you’re on.

You can also integrate a payment processor of your choice for an additional transaction fee.

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.

Square POS has no monthly fee. Square also offers two paid plans if you want advanced inventory features.

Square’s pharmacy POS features include:

• Free POS app: Square’s base POS system includes strong built-in tools for payment processing, inventory management, and customer tracking at no cost.
• Healthcare integrations: Works with apps like DrChrono EHR & RCM, Remedly, IntakeQ, and Reference Health Payments for medical billing and patient management.
• FSA/HSA acceptance: Pharmacies can accept FSA and HSA cards automatically if they have an eligible merchant category code (MCC).
• Scalability: Even large healthcare companies such as QuigMeds use Square’s technology to manage pharmacy POS operations.

Square sells POS hardware for iPad as well as its proprietary Square Register and Square Terminal; you can also source your POS hardware yourself.

Square accounts come with a free card swiper, though most pharmacies will want a more secure chip and tap reader, which you can use with an iPad or Android tablet.

Square charges a flat rate of 2.4% – 2.6% + $0.15 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.

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 may result in account stability issues for certain businesses.

CashierLive’s pharmacy plan is quote-based, but the company promotes it as offering the best value in the industry with no hidden fees.

While pricing for the pharmacy plan isn’t published, CashierLive’s standard retail package starts at $75/month, making it one of the more affordable POS options for small to midsize pharmacies.

CashierLive’s best pharmacy POS features include:

• Pharmacy-Specific Tools: Built with the needs of pharmacies in mind, including prescription sales tracking, inventory control, and compliance reporting.
• SIGIS Compliance: The first web-based SIGIS-compliant POS system, making FSA and HSA payment acceptance simple and secure.
• Cloud-Based System: Unlike most locally installed pharmacy POS systems, CashierLive runs in the cloud, giving you flexibility, mobility, and fewer maintenance costs.
• Pharmacy Software Integrations: Seamlessly integrates with key pharmacy platforms such as SpeedScript, HBS, Carepoint, RNA, and MethCheck (for pseudoephedrine sales).
• Affordable Alternative: Provides the essential tools of a full-featured pharmacy POS system at a fraction of the cost of traditional, on-premise systems.

CashierLive can run on iOS, Android, or a computer, which gives you the option to source hardware components yourself.

The company offers hardware bundles. However, pricing is expensive, so you may be better off sourcing your own hardware.

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

CashierLive 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.

Clover offers a variety of plans, with higher tiers offering more features.

Clover’s best features include:

• Easy Setup & Training: Plug in your POS hardware, activate your account, and start taking payments right away — no complicated setup or lengthy onboarding required.
• Simple Payment Acceptance: Ideal for pharmacies that need straightforward payment processing without complex add-ons or custom workflows.
• Flexible Integrations: Clover’s open REST API allows you to connect compatible third-party applications for expanded functionality.
• HSA/FSA Acceptance: While Clover itself isn’t IIAS-compliant, pharmacies with eligible MCC codes (5912 or 5122) can still accept HSA and FSA cards for qualifying purchases.

Clover’s hardware includes its flagship Clover Station POS. If you want a customer-facing screen, you can upgrade to the Clover Station Duo. Other hardware options include the Clover Mini and the mobile Clover Flex.

If you purchase your system directly from Clover, payment processing fees start at 2.3% – 2.6% + $0.10 per transaction, depending on your monthly software plan.

Various other entities also sell Clover with different (and often more expensive) payment processing structures.

Hundreds of different merchant service providers sell Clover, and not all of them are reputable.

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.