Pharmacy POS System

Pharmacy-specific POS software helps keep you organized, eliminate human error, and streamline workflow.

The last thing you want to do is invest in a system that doesn't have the aspects required to run your pharmacy smoothly.

That's where we come in.

We're here to review our 5 favorite pharmacy POS systems so that you can make an informed buying decision and get the exact features and functions that you need. 

Let's dive in.


Top Features

Best For

$29 per month starting

Website development, eCommerce integrations, age verification apps

eCommerce capabilities

$69 per month starting

Loyalty programs, customer management, vendor management

Top-of-the-line retail-centric features


Web-bad SIGIS-compliant system, prescription wholesaler purchase ordering

Pharmacy software integrations

$39.95 per month

Tons of hardware options, healthcare-friendly payment processor integration, accepts HSA and FSA

Hardware integrations


App integrations, EHR medical billing integration, chip and tap reader

Pharmacies on a budget

The Top 5 POS Pharmacy Companies

Shopify POS

Shopify is one of the best point-of-sale systems for pharmacies that use an online ordering system, thanks to its robust eCommerce capabilities.

However, it's also a complete solution for brick-and-mortar businesses. If you have a Shopify website and the right developer, there's almost nothing you can't do. We highly recommend Shopify Plus to pharmacy owners, as it has a history of powering multi-location enterprise-level pharmacies online, such as Lloyd's Pharmacy and Meagher's Pharmacy.

On the other hand, even if you run a small pharmacy, you'll find several unique features and eCommerce integrations that you can use to sell in-person or through your online store, including Retail Management Solutions, SnapRX, and other apps for age verification.

The pricing for Shopify runs from around $29 to $299 monthly, depending on your needs. You'll have to upgrade to Shopify Pro if you want access to the advanced invecost management features. This runs an extra $89 per month. If you only need mobile processing, you can go with the Shopify Lite plan, which costs $9 per month.

The payment processing fee, which is called Shopify Payments, uses Stripe. Depending on the plan you choose, rates range from 2.3% to 2.7%. If you already have a payment processor you work with, you have the option to integrate it into your Shopify system for an additional fee.

Shopify sells hardware in bundles or as individual components. If you prefer, you can obtain your own Android or iPad POS hardware. The most affordable bundle in Shopify's lineup is $219, giving you access to a card reader and a 9.7" iPad.


  • Great for adding eCommerce capabilities
  • Accepts FSA and HSA payments
  • Already successfully used by several online pharmacies


  • Offline mode is quite limited

If advanced retail features are what you're after, we highly recommend looking into Lightspeed. This system is best for non-prescription inventories.

With this cloud-based point of sale software, you'll get access to several advanced retail features, including eCommerce, accounting, loyalty programs, customer management, vendor management, inventory tracking, and much more.

It is one of the most flexible pharmacy management systems out there, all thanks to its open API, allowing you to customize your system with third-party software integrations.

The least expensive hardware option required to run Lightspeed's top-tier pharmacy POS software is an iPad.

Fees for Lightspeed range from about $69 to $199 per month if you have a single register. However, if you have a large business with multiple locations, you can take advantage of the company's quote-based pricing system.

The payment processing works via Lightspeed Payments, which has a 2.6% + $0.10 rate. If you want to use a different payment processor, you're in luck, as Lightspeed is compatible with several payment processors, including 2Accept, Vantiv, TSyS, and more. One great thing about Lightspeed is that you can choose to forego a processor altogether and use a separate system to handle payments.

Note that Lightspeed is an iPad POS system, and the pricing they provide for hardware is quote-based. However, if you'd like to continue using your own POS hardware, or would simply rather source it yourself, Lightspeed makes it easy to integrate.


  • Integrates with several third-party delivery apps
  • Quality supply chain and vendor management tools
  • Advanced reporting and inventory tracking


  • No pharmacy software integrations right out of the box

If you're in the market for a POS system with several pharmacy software integrations, then the Cashier Live point of sale system is a great choice.

One of the major benefits of this software is that it comes with built-in software integrations that work with other pharmacy systems.

Cashier Live was the pioneer in SIGIS-compliant POS systems.

Typically, if you need pharmacy-specific POS features, they can be very expensive and tend to have local installation requirements. 

The beauty of Cashier Live is that it acts as a wonderful cloud-based alternative. The premier pharmacy industry integrations for Cashier Live include MethCheck, RNA, Carepoint, HBS, and SpeedScript.

The pricing for Cashier Live is completely quote-based, though there are many that say this system offers unbeatable value. You won't have to deal with hidden fees either. It might be worth noting that the standard package is $75 per month, which is a fairly reasonable price. Cashier Live also offers a 2.7% flat rate for each in-person transaction, though it does not integrate with third-party payment processing.

You can run Cashier Live on a number of hardware components, including a computer, Android device, or iOS device. It is worth noting that Cashier Live's hardware is pretty expensive. For example, the PayPoint POS hardware they provide costs $2,599.


  • Dedicated pharmacy plans
  • Purchase ordering for prescription wholesalers
  • Can integrate with other pharmacy management systems


  • Hardware is very expensive

Clover might just be one of the easiest systems to get started with, which is great if you've found yourself struggling to train employees in the past.

The moment you receive your hardware, all you have to do is plug it in, go through the short activation, and you're good to go.

The system is exceptional for accepting basic payments.

Note that while it doesn't come with many features specific to pharmacies right off the bat, you can use the REST API to integrate with applications under the REST-ful suite.

You can also accept FSA and HSA cards using Clover as long as you have an eligible MCC code.

We recommend going with the Clover Register Plan, which costs $39.95 per month. For each additional terminal, you'll pay $9.95 per month. You can go with the Clover No Hardware plan, which goes for $10 per month, though most pharmacy owners might find that this doesn't provide the necessary support to run a brick-and-mortar business.

One place where Clover really shines is with its hardware. The least expensive option is the Clover Flex, which goes for $499, though you can upgrade to the Clover Mini for $749. If you want access to the best features and the most robust system, we recommend going with the Clover Station Solo or the Clover Station Duo. The main difference is that the Duo comes with a customer-facing display.

As for processing rates, the fees range from around 2.3% to 2.6% + $0.10 for in-person transactions. However, these rates only apply if you purchase through Clover. If you choose to purchase through a third-party provider, your payment processing rate may be much more expensive.


  • Integrates with payment processing systems that are healthcare-friendly
  • Unique plug-and-play design
  • Accepts HSA and FSA using Clover Payments


  • Cannot use proprietary hardware with other systems

Though it may come as a surprise, Square offers one of the best POS systems for pharmacies who are looking to get started.

This is because the first tier of Square doesn't cost a dime. You can upgrade to Square for Retail if you need more advanced features, such as inventory management, which costs $60 per month.

However, the free system really shines, offering tons of functionality.

Not only does the company offer easy-to-use payment processing, but you'll also find plenty of third-party app integrations to enhance the functionality of your business. Some of the best pharmacy-specific features include Reference Health Payments, IntakeQ, Remedly, and DrChrono EHR & RCM.

It's also worth noting that Square includes HSA and FSA payments right off the bat. All you need is a merchant category code.

Square has a flat rate payment processing system that works at 2.6% + $0.10 for in-person transactions. However, if your business earns more than $250,000 monthly, Square offers custom enterprise pricing. One downside is that you can not use a third-party payment processor if you go with Square.

The company also offers some pretty solid hardware options, including the Square Terminal at $49 and the Square Register at $799. You can source your hardware on your own if you choose. You'll be happy to know that every Square account comes bundled with a card swiper for free. However, most pharmacy owners opt for the chip and tap reader, which costs $49. The beauty of this chip and tap reader is that you can plug it into any Android or iPad tablet.


  • Medical billing software integration
  • Free business website included
  • Free POS app


  • Cannot use a third-party payment processor

FAQ: What Should I Be Looking For in a POS System For My Pharmacy?

Inventory Management

While inventory management is an important component for any business, it is even more crucial for a pharmacy. With a modern high-quality POS system that provides solid inventory management, you can record your total sales and billing details with each transaction.

Beyond that, a robust system like this will provide you with stock level visibility, sending you alerts when drug stock is running low.

Integration Capabilities

Your software should help streamline your workflow in every way, so that you can focus on the more important aspects of your business. However, if your software is unable to integrate with the other systems, you'll have a hard time enhancing your workflow. Some of the most commonly used systems in this industry include electronic medical records (EMR) software and billing and invoicing.

Look for integration capabilities when researching POS systems to use for your business.

Customer Support

The last thing you want is to be on your own when bumps in the road come along.

From the installation process to potential troubles down the line, having reliable vendor support is paramount.

Make sure that the system you choose has the backing of a professional support team to help troubleshoot when things go wrong.

You might also want to see if the company you are going with offers training support right off the bat.

Free POS Systems Quotes from

Additional Features

On top of the features we discussed for individual systems, there are a few extra features you should consider looking for in a quality POS solution. These include:

  • Prescription Management: Quality management software can help you process and manage multiple drug prescriptions simultaneously.
  • Automatic Refills: To increase the efficiency of your healthcare service, you can automate your refills.
  • Barcode and Label Scanning: To enable product tracking and ensure accurate pricing, you can use barcode and label scanning to record details about each product.
  • E-Prescriptions: With an e-prescribing system, you can accept or fill electronically submitted prescriptions.
  • Electronic Signature Capture: You can use this feature to request electronic signatures and have customers electronically sign documents.

The Bottom Line - Which of These Is Right for Me?

With the right POS system for your pharmacy, you'll be able to increase the efficiency of your sales, whether in-person or online, build stronger relationships with customers, and access a full suite of high-end tools and features that will make your life as a business owner much simpler.

We hope that you've found these reviews helpful in narrowing down your decision. Now it's all about finding the right provider to purchase your POS solution through.

We understand that getting quotes from different providers can be incredibly time-consuming. Our service provides FREE quotes from multiple POS providers based on your needs and budget.

Answer the few quick questions below to let us know what you're looking for!

Tyler Connaghan Author

Tyler Connaghan

Contributing Author