athenahealth vs eClinicalWorks vs Practice Fusion: 2026 Comparison

Choosing an EHR system feels a lot like choosing a phone plan — the options all look similar on paper, the pricing is confusing, and you won’t know if you made the right call until you’re locked in. Except with an EHR, the stakes are higher: your staff’s productivity, your billing revenue, and your HIPAA compliance all ride on this one decision.

If you’re running a small medical practice in Central Florida and you’ve narrowed your search to athenahealth, eClinicalWorks, or Practice Fusion, you’re looking at three of the most common platforms for practices under 10 providers. This guide breaks down what each one actually delivers — the good, the bad, and the stuff the sales rep won’t mention.

Quick Overview: What Makes These Three Different

Before we dive into the details, here’s the fundamental difference between these platforms:

• athenahealth — Cloud-based, premium-priced, strong on billing and revenue cycle management. Positions itself as the “Apple” of EHR systems.
• eClinicalWorks (eCW) — Feature-rich and customizable, mid-range pricing, steep learning curve. The “Android” of EHR — powerful if you invest the time.
• Practice Fusion — Simple, affordable, web-based. The budget-friendly option for small practices that need something straightforward.

Side-by-Side Comparison Table

athenahealth: Detailed Breakdown

Pricing

athenahealth uses a percentage-of-collections model — typically 4% to 7% of what they help you collect. For a practice collecting $500,000 a year, that’s $20,000 to $35,000 annually. It sounds expensive, and it is. But the argument is that their billing and revenue cycle management (RCM) tools will help you collect more money than you would on your own, offsetting the cost.

There’s no large upfront implementation fee for most small practices, which helps with cash flow during the transition.

Ease of Use

This is where athenahealth shines. The interface is clean, modern, and designed so that front desk staff and medical assistants can learn the basics in a few days, not weeks. Charting workflows are logical. The system doesn’t feel like it was built in 2005 (unlike some competitors).

Your office manager will appreciate that the billing dashboard shows you exactly where claims are stuck and why — no digging through cryptic reports.

Key Features

• Revenue cycle management: athenahealth’s billing engine is its strongest asset. It handles claim scrubbing, denial management, patient statements, and follow-up — all automatically. Many practices report a 5–10% increase in collections after switching.
• Patient engagement: Online scheduling, automated appointment reminders, patient portal with messaging, and digital intake forms.
• Interoperability: Connects to the CommonWell Health Alliance and Carequality networks, so you can exchange records with hospitals, labs, and other practices.
• Automatic updates: Being cloud-based, athenahealth pushes regulatory updates automatically — helpful when CMS changes billing rules or quality reporting requirements.

Pros

• Best-in-class billing and collections automation
• Intuitive user interface that reduces training time
• No upfront cost — pay as a percentage of collections
• Strong patient portal and engagement tools
• Automatic regulatory and compliance updates

Cons

• Most expensive option long-term (that percentage adds up)
• Customization is limited compared to eClinicalWorks
• Customer support has gotten mixed reviews in 2025–2026 as they’ve scaled
• Reporting tools are good but not as flexible as eCW’s
• Percentage-based pricing means your costs go up as your revenue increases — you’re penalized for success

Best For

Practices that want to maximize collections and minimize billing headaches. If your biggest pain point is insurance denials, slow payments, and billing chaos, athenahealth is the strongest choice. Particularly good for primary care and family medicine.

eClinicalWorks: Detailed Breakdown

Pricing

eClinicalWorks charges $449 to $599 per provider per month for their cloud-based solution, depending on the package and features you select. A 3-provider practice would pay roughly $16,000 to $21,500 per year. They also have an on-premise option, though most new customers go cloud.

Important: eCW typically requires a 3-year contract commitment, and early termination fees can be significant. Make sure you negotiate this before signing.

Ease of Use

This is eClinicalWorks’ weakest point. The system is powerful, but the learning curve is steep. Expect 2–4 weeks of focused training before staff are comfortable, and 2–3 months before workflows feel smooth. The interface has improved in recent versions, but it still feels busy and cluttered compared to athenahealth.

That said, once your staff learns the system, the customization pays off. You can build templates and workflows that match exactly how your practice operates — which saves time in the long run.

Key Features

• Customizable templates: Build note templates for virtually any specialty. This is a massive advantage for multi-specialty practices or any practice with unique documentation needs.
• healow patient portal: A dedicated patient app for scheduling, messaging, telehealth, and accessing records. healow has one of the higher patient adoption rates among EHR portals.
• Population health tools: If you participate in value-based care programs or quality reporting (MIPS/MACRA), eCW has built-in analytics and tracking.
• Telehealth: Integrated video visits with healow TeleVisits. No separate platform needed.
• Interoperability: Connects to Carequality, supports FHIR APIs, and has direct messaging capability for exchanging records with hospitals and labs.

Pros

• Highly customizable — adapts to virtually any specialty
• Comprehensive feature set in one platform
• Strong telehealth and patient engagement tools (healow)
• Good for practices planning to grow
• Pricing is fixed per provider — costs don’t increase with revenue

Cons

• Steep learning curve — plan for extended training
• 3-year contracts are standard and hard to negotiate down
• History of a major DOJ settlement in 2017 ($155 million) over data integrity issues — they’ve addressed the problems, but it’s worth knowing
• Customer support can be slow, especially for non-urgent issues
• Implementation takes 10–16 weeks for most small practices

Best For

Multi-specialty practices, growing practices with 3–10 providers, and practices that need deep customization. If you’re a specialty practice (dermatology, orthopedics, cardiology) and need templates tailored to your exact workflow, eCW gives you the most flexibility.

Practice Fusion: Detailed Breakdown

Pricing

Practice Fusion is the most affordable option at $149 per provider per month. A solo provider pays about $1,788 per year, and a 3-provider practice pays roughly $5,364 per year. No long-term contract required — month-to-month is available.

They also offer a free trial period, so you can test before committing. There’s no large upfront cost, making this the most accessible option for brand-new practices or practices converting from paper for the first time.

Ease of Use

Practice Fusion was designed with simplicity in mind, and it shows. The interface is clean and minimal. Front desk staff can usually get comfortable in 1–2 days. The charting workflow is straightforward — it won’t overwhelm new users.

The flip side is that simplicity means fewer features. If you need something the system doesn’t do out of the box, you’re mostly out of luck.

Key Features

• Charting: Basic but functional charting with templates for common visit types. Works well for primary care, urgent care, and general practice.
• E-prescribing: Built-in electronic prescribing, including controlled substances (EPCS).
• Lab integration: Connects to major lab networks for electronic ordering and results.
• Patient portal: Basic portal for patients to access records and communicate with the practice.
• Web-based: Runs entirely in a browser — no software to install, works on any device with internet access.

Pros

• Most affordable option — by a wide margin
• Easiest to learn and implement
• No long-term contract
• Runs in a browser — works on any computer or tablet
• Good for practices transitioning from paper records

Cons

• Limited features compared to athenahealth and eCW
• Billing is basic — you’ll likely need a separate billing solution or clearinghouse
• Limited customization options for specialty practices
• Interoperability is weaker — fewer health information exchange connections
• Reporting capabilities are minimal
• Owned by Veradigm (formerly Allscripts) — the parent company’s long-term strategy for Practice Fusion has been uncertain

Best For

Solo providers, brand-new practices, and practices making their first move from paper to digital. If you need something simple, affordable, and quick to implement, Practice Fusion gets the job done. Not ideal for practices that plan to grow beyond 3–4 providers.

Implementation: What to Actually Expect

The sales demo always makes implementation look smooth. Here’s what it actually looks like:

athenahealth (8–12 weeks)

• Weeks 1–2: Project kickoff, data gathering, workflow analysis
• Weeks 3–6: System configuration, data migration from your current system
• Weeks 7–10: Staff training (usually 3–5 training sessions)
• Weeks 11–12: Go-live with support, parallel running if needed

eClinicalWorks (10–16 weeks)

• Weeks 1–3: Project planning, workflow mapping, template customization
• Weeks 4–8: System build, data migration, interface setup with labs and pharmacies
• Weeks 9–14: Extended training (plan for 6–10 training sessions — this system requires more)
• Weeks 15–16: Go-live with support team

Practice Fusion (2–4 weeks)

• Week 1: Account setup, basic configuration
• Week 2: Data entry (limited migration tools — some manual work may be needed)
• Weeks 3–4: Staff training (1–2 sessions) and go-live

A Word About Data Migration

Moving patient records from your current system — whether that’s paper charts, another EHR, or a combination — is the most underestimated part of any EHR switch. Budget extra time and consider working with an IT services provider who has experience with medical data migration. Botched migrations lead to missing records, which creates both patient safety and HIPAA compliance risks.

Training: The Hidden Cost

Every EHR vendor will tell you training is “included.” What they don’t tell you is the cost of lost productivity while your staff learns a new system.

For a 10-person practice, the productivity loss during an eClinicalWorks implementation can easily cost $10,000–$20,000 in reduced patient volume. Factor this into your total cost comparison.

Interoperability: Can It Talk to Other Systems?

Your EHR doesn’t exist in a vacuum. It needs to exchange data with hospitals, labs, imaging centers, pharmacies, and referring physicians. Here’s how each platform handles this:

• athenahealth: Connects to CommonWell Health Alliance and Carequality, giving you access to the largest health information exchange networks. Lab orders, results, and hospital records flow in and out smoothly in most cases.
• eClinicalWorks: Connects to Carequality and supports modern FHIR APIs. Also has direct messaging for secure document exchange. Good interoperability, though initial setup of interfaces can be time-consuming.
• Practice Fusion: Basic lab integrations work, but broader health information exchange is limited. If you frequently receive records from hospitals or need to participate in an HIE (Health Information Exchange), Practice Fusion may fall short.

Interoperability matters more than you might think. If your EHR can’t pull in a patient’s hospital discharge summary automatically, your staff is calling, faxing, and manually entering data — which costs time, money, and increases the risk of errors.

HIPAA and Security: What to Verify

All three platforms are HIPAA-compliant and sign Business Associate Agreements (BAAs). But “HIPAA-compliant” is a baseline, not a guarantee. Here’s what to check:

• Data encryption: All three encrypt data in transit and at rest. Verify this is documented in their BAA.
• Access controls: Make sure you can set role-based permissions — the front desk shouldn’t have the same access as a provider.
• Audit logs: All three provide audit logging. Verify that logs capture who accessed what record and when.
• Backup and recovery: Cloud-based EHRs handle backups, but ask about their recovery time objective (RTO) — how long it takes to restore service after an outage. You’ll also want your own backup strategy for any data stored locally.

Regardless of which EHR you choose, your overall cybersecurity posture needs to extend beyond the EHR itself. Your network, endpoints, email, and staff training all need to be locked down. An EHR is only as secure as the environment it runs in.

How to Choose: A Decision Framework

Here’s a straightforward way to decide which platform fits your practice:

Choose athenahealth if:

• Your biggest headache is billing and collections
• You want the most user-friendly interface
• You’re comfortable paying a premium for a premium experience
• You’re a primary care, family medicine, or internal medicine practice
• You want automatic regulatory updates without IT involvement

Choose eClinicalWorks if:

• You’re a specialty practice that needs custom templates and workflows
• You plan to grow from 3 providers to 10+ in the next few years
• You want the most features in one platform
• Your staff is tech-savvy enough to handle a steeper learning curve
• You want fixed, predictable costs that don’t scale with revenue

Choose Practice Fusion if:

• You’re a solo provider or very small practice (1–3 providers)
• Budget is your primary concern
• You’re transitioning from paper for the first time
• You need something up and running in weeks, not months
• You don’t need advanced billing, reporting, or interoperability features

What Your IT Setup Needs to Support Any EHR

No matter which EHR you choose, your IT infrastructure needs to be solid. A cloud-based EHR running on an unreliable network is still unreliable. Before you implement any of these platforms, make sure you have:

• Reliable internet: A business-grade connection with a failover (backup internet). If your internet goes down, your EHR goes down.
• Updated workstations: Old, slow computers will make even the fastest EHR feel sluggish. Budget for hardware that’s 4 years old or newer.
• Network security: Endpoint protection on every device, email security to prevent phishing, and a properly configured firewall.
• Backup strategy: Even with a cloud EHR, you need local and cloud backups for any data stored on-premise.
• IT support: An IT help desk your staff can call when something isn’t working — because it will happen.

Need Help Choosing or Implementing an EHR?

iTech Plus helps medical practices across Tampa, Orlando, Lakeland, and Central Florida evaluate, implement, and support EHR systems. We don’t sell EHR software — we help you make the right choice for your practice and make sure your IT infrastructure is ready to support it.

Whether you’re switching from one EHR to another, going digital for the first time, or just need someone to evaluate whether your current setup is working, we can help.

Schedule a free consultation or call us at (321) 221-7117 to talk through your EHR options with someone who understands both the technology and the healthcare side.