IRS Expands Pre-Filing Agreement Program to Support Research Credit Claims

MASSIE is excited to see the IRS release new updates to its Pre-Filing Agreement Program, reinforcing its commitment to proactive, cooperative compliance. As we’ve noted throughout the past year, the IRS continues to encourage more taxpayers, especially those claiming the R&D tax credit, to engage with the PFA process.

If your company is considering a Pre-Filing Agreement for research credit issues or other complex tax positions, contact Taylor Eiselin to explore how this program could reduce your audit exposure and improve certainty.

IR-2025-69, June 17, 2025

WASHINGTON — The Internal Revenue Service has announced a series of improvements to the PFA program, specifically aimed at enhancing certainty for large business and international (LB&I) taxpayers.

These enhancements reflect the IRS’s broader shift toward cooperative tax administration. By using PFAs, businesses can resolve high-stakes tax issues before filing their returns—minimizing audit risk and encouraging voluntary compliance.

What’s New in the IRS Pre-Filing Agreement Program

The IRS has introduced several changes that make it easier for taxpayers to understand, apply for, and benefit from a Pre-Filing Agreement:

A redesigned PFA program homepage with easier navigation, current program statistics, and quick access to dispute prevention resources.
Clear, step-by-step instructions for submitting a PFA request, including response time expectations and a guide to what happens after submission.
A dedicated PFA-eligible issues and documentation page to help companies evaluate whether their situation qualifies.
Updated guidelines to help businesses better align their PFA submissions with their tax return filing deadlines.

Why This Matters for R&D Tax Credit Planning

For companies planning to claim the research and development tax credit, the PFA program offers a valuable opportunity to confirm eligibility criteria with the IRS upfront—especially in light of increased scrutiny and documentation standards in recent years.

Pursuing a PFA can:

Offer clarity on qualified research activities (QRAs) before filing Form 6765
Limit the scope of future audits
Support stronger positions in case of controversy or refund claims

If your tax team is considering a Pre-Filing Agreement—or wants to better understand when it’s worth pursuing—our team at MASSIE is happy to help. Reach out to Taylor Eiselin to start the conversation.

Jason Massie, CPA, Esq.

As the Founder and President of MASSIE R&D Tax Credits, Jason is responsible for the quality, consistency, and integrity of our services. His strategic vision and leadership drive innovation within the company, encouraging collaboration and ne...