Pricing Pharmacy Software: Are There Hidden Costs?

• Not all pharmacy software includes the features that independent pharmacies need to succeed.
• Implementing a new pharmacy software system can come with additional expenses.
• Datascan offers an all-inclusive system with no hidden fees and award-winning support.

When independent pharmacy owners begin their search for the best pharmacy software, pricing is often one of the first questions that comes to mind. After all, your pharmacy software is hands-down the most important investment you’ll make in your business. But here’s the thing: not all vendors are upfront about what you’ll actually end up paying.

In fact, the world of pharmacy management software pricing can sometimes feel like navigating a maze. Many competitors lure in pharmacies with what appears to be a low monthly cost, only to tack on hidden fees later. The result? You may find yourself paying far more than you originally budgeted.  It’s important to understand exactly what you’re paying for and exactly what you’re getting.

At Datascan Pharmacy Software, transparency is key. Datascan has built a reputation as one of the top pharmacy software providers by offering clear, upfront, and honest pricing—without the nickel-and-diming practices that are all too common in the industry.

First, it’s important to break down the common costs of pharmacy management systems, where hidden fees often creep in, and how Datascan stands apart with transparent, all-inclusive pricing.

The True Costs of Pharmacy Software

Every pharmacy software system comes with a few standard costs. While they may vary by vendor, most pharmacies should expect the following:

1. Licensing Fees

This is the cost of obtaining the software license itself. Some vendors charge by the number of users and number of workstations, whereas Datascan includes an unlimited number of users and workstations.

2. Onboarding and Training

Pharmacy software is undoubtedly complex. Pharmacies need onboarding, setup, and staff training to ensure the system is used effectively. Some companies charge fees for training sessions or limit the number of hours included.  Datascan always includes initial training, as well as ongoing training for free.  This ensures that you and your staff are constantly up to date with new features, and have a comprehensive understanding of the pharmacy systems capabilities.

3. Data Conversion and On-site Training

If you’re switching from one pharmacy management software to another, the data conversion is often one of the biggest expenses. Moving prescription data, patient profiles, prescriber information, and inventory is handled with the help of a data conversion company– and isn’t always included. Some vendors upcharge conversions, which can cost your pharmacy thousands of dollars. Datascan, however, often offers pharmacies free data conversion, saving them significant upfront costs.

On-site training is often another exorbitant cost for a pharmacy.  Many pharmacy software vendors charge thousands of dollars to send staff on-site for only a few days.  Datacan staff come onsite typically Monday-Friday, and often includes the cost of on-site training for free, with minimal fees to cover travel-related costs for the staff.

4. Monthly Support and Maintenance

Every pharmacy software vendor charges a monthly service fee for support and ongoing system maintenance. This is expected, as pharmacy systems require continual updates to remain compliant with regulations and to integrate with third-party services such as Surescripts or pharmacy claims switching vendors.  This price varies from vendor to vendor and can range from affordable to astronomical.  

Datascan offers a ‘package price’ that includes not only your pharmacy software licences and maintenance, but many services that other vendors charge add-ons for, such as document management, or our patient-facing mobile application– they are included!

5. Transaction Fees

There are also transaction-based fees, such as electronic prescribing and insurance claims switching. While these are unavoidable in the industry, rates vary depending on the vendor.  It is important to understand these fees and be able to quantify your charges at the end of each month.  Datascan provides its clients with an easy-to-read breakdown and summary of charges each month for all costs related to the pharmacy management systems. 

Where the Hidden Fees Sneak In

Here’s where things get complicated– many vendors don’t include anything with their base pricing. Instead, they charge additional fees for features that should be standard in a pharmacy management system.

Often, you won’t even know about these hidden costs until you try to enable a feature. At that point, you’re locked in, and your “affordable” pharmacy software suddenly costs far more than expected.

Some of the most common hidden add-on costs include:

• Patient Mobile Apps – An essential in today’s digital-first world, but some vendors charge extra, often in excess of $100 per month, to offer a mobile app for patients.
• Delivery Applications – Many pharmacies rely on delivery, but delivery management tools are often sold as expensive add-ons.  These can cost your pharmacy upwards of $50+ per month.
• Third-Party Data Feeds – Want to share data with a partner platform? Some vendors make you pay just to access your own data.
• Document Management – Storing and managing scanned prescriptions, insurance cards, and other paperwork is crucial, yet many vendors add extra fees for this capability.
• Faxing – Still widely used in pharmacy, fax integration is another common hidden fee.
• Controlled Substance Reporting – Control reporting isn’t optional, yet some systems tack on fees for automated reporting. 
• After-Hours Support – You may find yourself paying a premium to get help outside of standard business hours.
• Compound capabilities – you may not offer compounded medications now, but if you decide to add it to your business model later, does the pharmacy system have this built in?
• LTC / Nursing — again, something you may add in the future –but does the pharmacy software have it built in, and is it free of charge?

These “nickel and dime” fees add up quickly. What seemed like an affordable monthly rate can balloon into something significantly higher once all the must-have features are factored in.

Be Careful: PioneerRx’s “RX Usage Fee”

One example that stands out in the industry is PioneerRx. They charge an “RX usage fee” for every prescription picked up at the point of sale– every one– including cash prescriptions!

This fee may not sound significant at first, but when calculated out, and added to the switching cost, it comes to nearly 10 cents per prescription on insurance-based claims. This is an astoundingly high rate. Pharmacies often don’t realize how much this adds to their overall expenses until it’s too late.

This is why it’s so critical to ask detailed questions about pricing and request a side-by-side comparison. Datascan encourages pharmacies to bring competing quotes to the table so you can clearly see how the costs stack up—and where the hidden fees lie. Compare pharmacy systems vendors side by side, for price, customer satisfaction (online ratings), and technology.

Datascan’s Approach: Transparent Pricing with No Hidden Fees

Datascan has taken a very different approach to pricing.  As one of the best pharmacy software providers in the industry, Datascan believes that pharmacies deserve full visibility into what they’re paying for.

Here’s what sets Datascan apart:

• All-Inclusive Base Pricing – Features that competitors charge extra for—like mobile apps, delivery tools, document management, faxing, and after-hours support—are included in Datascan’s base pricing.
• Free Data Conversion (for many pharmacies) – Making the switch shouldn’t come with a giant cost. Datascan helps many pharmacies convert data at no cost.
• Clear Monthly Support Fees – You know upfront what you’ll pay each month for pharmacy software support and maintenance, with no surprise charges.
• No Usage-Based Nickel and Diming – Unlike competitors, Datascan doesn’t add fees for “RX Usage.”
• Honest Comparisons – Datascan helps pharmacies review competitor quotes line by line so you can see exactly what you’re paying for.

Why Transparency Matters

Independent pharmacies are already struggling with shrinking reimbursement rates, DIR fees, and staffing challenges. The last thing an independent pharmacy needs is surprise costs from its pharmacy management software.

Transparent pricing not only protects your bottom line but also builds trust. When you know exactly what you’re paying for, you can budget more effectively and focus on what really matters: building a better and more profitable pharmacy.

Datascan’s approach to pricing reflects its larger philosophy: providing pharmacies with the tools, support, and service they need to succeed, without the games or hidden fees.  Datascan has been laser-focused on the success of independent pharmacy for over 4 decades.

Final Thoughts

When it comes to choosing the best pharmacy management software, price is about more than just an upfront number on paper. It’s about understanding the true costs—both upfront and ongoing—of the system you’re investing in.

Hidden fees for features like mobile apps, delivery tools, or even control reporting can significantly increase your total spend. 

Datascan stands out as one of the top pharmacy software providers because of its transparent pricing model, all-inclusive features, and commitment to helping independent pharmacies thrive. With no hidden fees and clear, upfront pricing, Datascan makes it easy for pharmacies to budget confidently and invest in a software system that truly delivers value.

If you’re evaluating software for pharmacies, take the time to ask the right questions about pricing. And most importantly, ask Datascan to help you compare—so you can be sure you’re not paying for hidden costs you never expected.