Prior authorization in Practice Fusion runs on built-in electronic prior authorization (ePA). When a prescription needs a PA, the EHR flags it while you prescribe and routes the payer's question set to your Tasks, the patient's Timeline and the Prior authorizations report. The feature is included at no additional cost, which matters for the small independent practices Practice Fusion is built for.

You're probably spending a lot of time using this feature. The 2025 AMA Prior Authorization Physician Survey found physicians complete an average of 40 prior authorizations per week, consuming 13 hours of physician and staff time.

This guide walks through the four ways Practice Fusion practices get PAs done, step by step: what each covers, where each stops, and how to combine them.

The 4 Ways to Do Prior Authorizations in Practice Fusion

Option 1: ePA at the Point of Prescribing

This is the default path. Automatic ePA is on unless someone turns it off under Settings, e-Prescribing, Electronic Prior Authorization.

How to submit an ePA when you e-prescribe (per Practice Fusion's help center):

1. Order the medication. Choose it, click Add to order, then Review order. Add a related diagnosis; leaving it off can delay PA processing.
   
   

2. Watch for the alert. A "Prior authorization required" flag appears under Cost saving alternatives if the patient's plan requires one.
   
   

3. Set Dispense As Written (DAW) deliberately. Check DAW if the brand must be dispensed. If it's unchecked, Practice Fusion checks the generic and starts a PA only if the generic needs one.
   
   

4. Click Process eRx. The patient's Timeline shows Awaiting PA Form until the payer sends its question set.
   
   

5. Complete the question set. When the status changes to Incomplete, a task appears. Open it from Tasks, the Timeline or the Prior authorizations report, answer each question (answers auto-save, and you can browse the chart while you work), attach a document if requested, review and click Submit.

Any member of the practice can complete the form, not just the prescriber. Route PA tasks to one staff member so question sets don't sit in a provider's queue.

What each status means:

One denial item you should know about is that if the payer's note describes what it would approve, such as a lower quantity, cancel the original prescription and send a new one that matches. That triggers a fresh PA.

Option 2: Manually Initiated and Pharmacy-Initiated PAs

Not every PA starts with an eRx. You can request one manually when the alert didn't fire, when a pharmacy reports a rejection, or before you prescribe.

From the patient's chart (per Practice Fusion's help center):

1. Open the Actions dropdown and select Add prior authorization.
   
   

2. Pick the medication. Choose a new one or one from the patient's eRx list. For a new medication, fill in Dispense, Unit and Days Supply; for a previous eRx, those fields auto-populate.
   
   

3. Confirm the prescribing provider and PBM, then click Request PA.

From the Prior authorizations report: go to Reports, open Prior authorizations, click Add Prior Authorization, choose the patient and medication, and click Request PA. Either way, the request then moves through the same statuses as Option 1.

Pharmacies can also initiate PA requests through Practice Fusion when they find a PA requirement after the eRx is sent. Those requests land in the same Tasks, Timeline and report, so you complete them the same way.

When the payer isn't connected electronically: Practice Fusion's ePA vendor converts the payer's form into the same electronic question format, so the workflow doesn't change. Expect responses in 1 to 5 business days rather than minutes.

Where Practice Fusion's Native ePA Stops

Options 1 and 2 share the same limits, all documented in Practice Fusion's help center:

• Manual answers: staff still read the chart and answer every question set.
  
  

• One attachment: each PA allows a single document of up to 10 MB.
  
  

• No edits after submission: a mistake means canceling and starting over.
  
  

• Limited appeals: the Appeal button appears only when the payer supports electronic appeals.
  
  

• Closed dead ends: a Closed status (patient not found, PA already approved or denied, or no ePA support) leaves next steps to your team.
  
  

• Prescriptions only: ePA covers drugs under the pharmacy benefit, not referrals or imaging.
  
  

• Easy to switch off: with the ePA toggle off, PA alerts, tasks and pharmacy-initiated requests all disappear.

Option 3: CoverMyMeds Portal

CoverMyMeds is the ePA portal most pharmacies use, and it's free for prescribers and their staff. Some Practice Fusion practices keep a CoverMyMeds account for requests that start outside the EHR, such as a pharmacy fax with an access key.

Running both has a known side effect. Practice Fusion's help center has a dedicated article on duplicate prior authorizations in the CoverMyMeds portal: practices that use ePA inside Practice Fusion and also have a CoverMyMeds account can see the same PA task in both places. The fix is to remove prescriber verifications in CoverMyMeds or turn off its notifications, so the work happens in one queue.

Best for: Pharmacy-initiated requests that arrive with a fax key, and practices that already work in the portal.

Where it stops: It's a separate login with its own queue, and it only transmits requests: staff still answer questions, gather evidence and work denials. Starting PAs in the EHR at prescribing is usually faster; CoverMyMeds' own research found patients access medications 13.2 days sooner on average when PAs begin at the provider's office.

Option 4: AI-Native Automation via API (Develop Health)

Develop Health is an AI platform that automates the full pharmacy-benefit PA cycle, from benefit verification through appeals.

Develop Health works with Practice Fusion data through two APIs. Practice Fusion publishes a certified FHIR R4 API with SMART app launch, system-level access and bulk export, and developers register through its marketplace. Develop Health's REST API handles benefit verification and PA requests. Your engineering team or an integration partner connects them:

1. New prescriptions are read from Practice Fusion, along with coverage, conditions, labs and documents, and sent to Develop Health as a benefit verification or PA request with clinical evidence attached.
   
   

2. Develop Health prepares the PA and either submits it and handles payer follow-up for you (delegated) or sends your reviewer a link to approve it first (non-delegated).
   
   

3. Webhooks push every status change to your systems as it happens.

You should be aware, Practice Fusion's FHIR API is read-only for clinical data, so determinations land in Develop Health's portal or your own systems rather than writing back into the chart. Providers still prescribe exactly as they do today.

What it automates that the options above don't:

• Coverage checks before the pharmacy rejection: real-time benefit verification returns coverage, PA requirements and out-of-pocket cost.
  
  

• Answers without manual chart review: AI pulls supporting clinicals from historical notes and labs, then fills payer question sets with cited documentation.
  
  

• Coverage beyond ePA rails: ePA where rails exist, AI phone calls and fax where they don't, with human fallback.
  
  

• The other half of the process: denial-reason analysis, AI-generated appeal letters and resubmission, including for payers without electronic appeals.

Develop Health reports an 83% reduction in medication-access admin work across hundreds of thousands of patients per month, plus a 14% lift in approval rates and prescription-to-approval cycle times cut from about 1.5 weeks to roughly 20 hours. In one case study, Arches Primary Care processed about 800 prior authorizations in six weeks, cutting turnaround from weeks to two days.

Pricing: Small per PA or per provider fee; free if sponsored by pharmacy or manufacturer.

Best for: Practice Fusion practices with high specialty-medication PA volume (GLP-1s, biologics) and access to technical help, in-house or through an integration partner.

Where it stops: It focuses on pharmacy-benefit PAs, it needs integration work without a native connector, and because the API is read-only, PA statuses live outside the Practice Fusion chart.

Side-by-Side: PA Options in Practice Fusion

Automate the PAs Practice Fusion's Native Tools Can't

Practice Fusion's native ePA is the right starting point, and every practice should use it. But the work that burns the most staff hours (answering question sets from the chart, chasing Closed and denied requests, appeals) still sits with your team. 

Develop Health automates that complete pharmacy-benefit cycle through an API that works alongside Practice Fusion, with no change to how providers prescribe. Book a demo to see how it fits your workflow.

Frequently Asked Questions

Does Practice Fusion have electronic prior authorization?

Yes. ePA is built into Practice Fusion at no additional cost and turned on by default. It covers prescription drugs under the patient's pharmacy benefit, flags PAs while you e-prescribe, and tracks every request in Tasks, the patient's Timeline and the Prior authorizations report.

Why didn't a prior authorization trigger in Practice Fusion?

Check three things. First, the ePA toggle under Settings, e-Prescribing, Electronic Prior Authorization: when it's off, PA alerts, tasks and pharmacy-initiated requests are all suppressed. Second, the DAW box: if it's unchecked and the generic doesn't need a PA, none starts. Third, a Closed status, which means the payer returned no question set. You can always start one manually with Add prior authorization.

Why do I see duplicate prior authorizations in CoverMyMeds?

If your practice uses Practice Fusion's ePA and your prescribers are also verified in a CoverMyMeds portal account, the same PA can show up in both places. Practice Fusion's help center recommends removing prescriber verifications or turning off notifications in CoverMyMeds.

How do I appeal a denied prior authorization in Practice Fusion?

Open the denied PA from the Timeline or the Prior authorizations report. If the payer supports electronic appeals, an Appeal button appears in the details; if not, contact the payer directly. If the denial note describes what the payer would approve, you can instead cancel the prescription and send a new one that matches.

How do I handle prior authorizations for referrals and imaging in Practice Fusion?

Outside ePA. Practice Fusion's ePA covers prescription drugs under the pharmacy benefit only, so referral, imaging and procedure authorizations go through each payer's portal, phone line or fax.