Flatiron's OncoEMR supports more than 4,700 providers across 1,600+ community sites of care, but Flatiron doesn't market a dedicated authorization-management module the way other EHRs, like athenahealth and Epic do. Most practices assemble their PA workflow from OncoEMR's documentation tools, payer portals, pharmacy partners and third-party automation.

In an ASCO member survey on prior authorization, 80% of oncology respondents said PA had contributed to disease progression for a patient, and payers took five business days on average to respond to a request.

This guide covers the four ways community oncology practices on OncoEMR get PAs done: what each handles, where each stops, and how they fit together.

Infusion vs. Oral Oncolytic PAs

Oncology runs two separate PA pipelines that rarely share tools. At a September 2026 House Oversight hearing on oral chemotherapy costs, a Northwestern oncologist testified that IV chemotherapy falls under the medical benefit and oral chemotherapy under the pharmacy benefit, with very different consequences for patients.

Medical-benefit PAs cover infused and injected therapies given in your clinic: chemotherapy regimens, immunotherapy and supportive infusions. They are billed by J-code, tied to the regimen ordered in OncoEMR, and submitted through payer portals or X12 278 transactions.

Pharmacy-benefit PAs cover oral oncolytics and other drugs patients take at home, such as tyrosine kinase inhibitors, PARP inhibitors and many supportive care medications. These go to the PBM, often require a designated specialty pharmacy, and carry cost-sharing that can stop a fill entirely. Testimony at the same hearing cited data showing patients facing more than $500 out of pocket were 4 times more likely to abandon an oral cancer drug than those paying $100 or less.

This guide focuses mainly on the pharmacy-benefit side.

How Third-Party PA Tools Connect to OncoEMR

When a vendor says it "works with OncoEMR," that can mean four very different things. The connection path decides whether PA status lands in your team's normal workflow or in yet another browser tab.

Ask every vendor two questions: which data it reads (structured fields only, or scanned pathology and visit notes too), and where determinations come back. Oncology PAs live or die on biomarker results and treatment history that often sit in unstructured documents.

The 4 Ways to Do Prior Authorization in OncoEMR

Most practices use more than one of these.

Option 1: OncoEMR's Built-In Tools, Flatiron Assist and Payer Portals

OncoEMR's contribution to PA happens upstream, at ordering. Flatiron Assist surfaces NCCN-concordant and practice-preferred regimens at the point of care, then captures concordance and other payer-required data elements in a structured format for PA documentation.

Regimen configuration helps too. OncoEMR regimen templates carry insurer-level settings, as shown in manufacturer build guides like the JEMPERLI OncoEMR regimen guide. Flatiron also reports that Tennessee Oncology used its ingredient drug substitution for 505(b)(2) drugs to improve adherence to insurer preferences and reduce time to treatment.

After that, staff take over. They log into payer portals, fax forms, call for status and track open requests in spreadsheets or shared inboxes.

Best for:

• Every OncoEMR practice, as the foundation. Clean, concordant documentation at ordering makes every downstream option work better.
  
  

• Medical-benefit infusion PAs, where regimen concordance drives approvals.

Where it stops:

• No electronic submission, payer status tracking or benefit verification.
  
  

• Denials and appeals are fully manual. In ASCO's survey, PA requests were escalated beyond the staff member who started them 34% of the time.

Option 2: ePA Portals (CoverMyMeds and Surescripts)

Electronic prior authorization (ePA) replaces fax for pharmacy-benefit PAs. Two networks dominate: CoverMyMeds, which is free to providers, and Surescripts, whose free Prior Authorization Portal serves practices without EHR integration. 

OncoEMR's certified e-prescribing relies on Surescripts and DrFirst. Flatiron doesn't publicly document an embedded ePA workflow, though, so many OncoEMR teams use these as standalone web portals. Ask your Flatiron representative what's enabled in your instance.

The most automated layer is Surescripts Prior Authorization Automation. As of May 2026 it supports 104 medications for 68,000 prescribers across 42 health systems, with an 18-second median approval when criteria are met. Deployments so far sit mostly in health systems, so check whether your setup and payers qualify.

Best for:

• Practices with low-to-moderate oral oncolytic volume that need to get off fax.
  
  

• Completing pharmacy-initiated PA requests quickly.

Where it stops:

• Staff still answer every question set, gather biomarker and treatment-history evidence, chase determinations and handle appeals.
  
  

• Payers are splitting between networks. Independence Blue Cross stopped accepting CoverMyMeds on August 1, 2025, so most practices need accounts on both.

Option 3: Hand Off to the Pharmacy Side

For oral oncolytics, many practices let someone downstream own the PA. It comes in three common versions:

• Specialty pharmacy: Most plans route oral oncolytics to specialty pharmacies, which can start the PA and request clinicals from your office.
  
  

• Medically integrated pharmacy (MIP): NCODA defines an MIP as a dispensing pharmacy within an oncology practice. The American Oncology Network's pharmacy, for example, handles benefit investigations, prior authorizations and financial assistance for its clinics. House Rx, in Flatiron's network, helps practices stand one up.
  
  

• Manufacturer hubs: Brand patient-support programs run benefit investigations, help with PA paperwork and connect patients to copay assistance for that brand's drug.

Best for:

• Practices without dedicated PA staff, where a free downstream partner beats an unstaffed queue.
  
  

• Larger groups with an MIP that want to keep oral oncolytic patients, data and follow-up in-house.

Where it stops:

• PA status lives in someone else's system. Practice staff have reported that specialty pharmacies don't always flag when a PA is needed, so denials surface late.
  
  

• Hubs work brand by brand, each with its own enrollment form and portal.
  
  

• An MIP moves PA work in-house rather than removing it. Someone still completes every form.

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

Develop Health automates the full pharmacy-benefit PA cycle, from benefit verification through appeals. It doesn't have a native OncoEMR integration. Instead, practices connect through the Develop Health API: REST endpoints run benefit verifications and submit PAs, and webhooks push status changes back as they happen.

In practice, your IT team or an integration partner sends prescription, insurance and clinical data from OncoEMR, for example through Flatiron's FHIR backend access or an HL7 feed. Statuses then route to wherever your team already works.

What it automates that the options above don't:

• Benefit verification before the patient leaves: Each request checks coverage, PA requirements and copay for up to seven drugs by exact NDC. In real-time mode, 80% of successful checks finish within 10 seconds. Harder plans fall back to AI phone calls (commonly 30-60 minutes) and human calls (usually within one business day).
  
  

• Evidence-backed forms: AI turns the patient's chart into a payer-ready submission, extracting biomarker results, staging and prior therapies from notes and labs with citations.
  
  

• Your choice of control: In the delegated model, Develop submits and handles follow-up. In the non-delegated model, your PA coordinator or pharmacist reviews the prefilled answers and evidence, edits and approves before anything goes to the payer.
  
  

• Submission, follow-up and appeals: ePA where rails exist, AI phone calls and fax where they don't, with human fallback. Denials get AI analysis and a generated appeal letter.

Across customers, Develop reports an 83% reduction in medication-access admin work and a 14% lift in approval rates. One customer moving off hub services cut prescription-to-approval time from about 1.5 weeks to roughly 20 hours.

Best for:

• OncoEMR practices with steady oral oncolytic and supportive-care volume and staff stretched thin.
  
  

• Teams that want automation without giving up clinical review.

Where it stops:

• Pharmacy benefit only. Infusion auths still need Option 1 or a medical-benefit vendor.
  
  

• With no native OncoEMR connector, plan for some integration work on your side or with a partner.

Side-by-Side: PA Options in OncoEMR

Automate the Oral Oncolytic PAs OncoEMR Can't

OncoEMR gives your team strong documentation at ordering. The hours go everywhere after that: checking coverage, pulling biomarker evidence into payer forms, chasing determinations and writing appeals. 

Develop Health automates that full pharmacy-benefit cycle through an API that works alongside OncoEMR, with no change to how your oncologists prescribe. Book a demo to see it in action.

Frequently Asked Questions

Does OncoEMR have built-in prior authorization?

Partly. Flatiron Assist captures concordance and payer-required data at ordering, and regimens can carry insurer-specific settings. Flatiron doesn't market a dedicated module for PA submission, tracking or appeals, so most practices pair OncoEMR with ePA portals, pharmacy partners or third-party automation.

Can I submit electronic prior authorizations from OncoEMR?

It depends on your setup. OncoEMR's certified e-prescribing relies on Surescripts and DrFirst, but Flatiron doesn't publicly document an embedded ePA workflow. Ask your Flatiron representative; otherwise, CoverMyMeds and the Surescripts Prior Authorization Portal are free standalone options.

How do third-party PA tools integrate with OncoEMR?

Through Flatiron's FHIR APIs, HL7 interfaces, the Flatiron Vendor Network, or document and fax workflows with no integration at all. API-first platforms like Develop Health receive the data your integration sends and return statuses by webhook, the same model we describe in our guide to prior authorization in Epic.

How long does an oncology prior authorization take?

Payers took five business days on average to respond in ASCO's member survey. Since January 1, 2026, CMS has required Medicare Advantage and Medicaid plans to decide standard requests within 7 calendar days and urgent ones within 72 hours, but those deadlines don't apply to drug PAs. End-to-end automation has cut prescription-to-approval time to roughly 20 hours for some Develop customers.

How much does prior authorization automation cost for an oncology practice?

ePA portals and manufacturer hubs are free to practices, and Flatiron Assist is licensed through Flatiron. Develop Health charges a small per-PA or per-provider fee, and access can be free when a pharmacy or manufacturer sponsors it.