My R&D Claim Was Rejected. Can I Appeal, Re-Submit, or Switch Advisor?

A rejected R&D claim under the merged R&D Expenditure Credit scheme means one of three things: HMRC opened a compliance check and issued a closure notice disallowing the claim; HMRC issued an amendment to your company tax return; or your adviser submitted a claim that HMRC has now challenged. Each scenario carries distinct options, and the clock starts running the moment you receive HMRC's decision.

Two-year amendment window, 30-day appeal deadline, right to HMRC internal review: these are the three numbers you need to know immediately. Missing any one of them may close options that cannot be re-opened.

What "Rejected" Actually Means in HMRC Terms

HMRC does not issue a single "rejection letter." What actually happens depends on the process that led to the disallowance.

Closure notice after enquiry. If HMRC opened a formal enquiry under Schedule 18 Finance Act 1998, they will close it by issuing a closure notice. The notice states HMRC's conclusion and any amendment to your return. This is the document that starts the 30-day appeal clock.

Discovery assessment. HMRC may issue a discovery assessment under paragraph 41 Schedule 18 FA1998 to recover tax from an R&D claim they believe was overclaimed, even outside a formal enquiry. This is also subject to 30-day appeal rights.

Informal challenge. In some cases HMRC writes informally during a compliance check requesting more information or signalling that they intend to disallow the claim. This is not yet a formal decision and there is nothing to appeal at this stage. You or your adviser should respond substantively within the timeframe given.

Knowing which document you have received determines your immediate next step. If in doubt, check whether the letter references an enquiry closure notice or is headed as a formal assessment.

Your Appeal Rights: The First-Tier Tax Tribunal

Once HMRC issues a closure notice or formal assessment, you have 30 days to appeal under section 31 Taxes Management Act 1970. The appeal goes to the First-tier Tax Tribunal (Tax Chamber), which is entirely independent of HMRC.

Before appealing to the tribunal, you can request an internal HMRC review under section 49A TMA 1970. Requesting a review pauses the 30-day tribunal clock while an HMRC officer who was not involved in the original decision reviews the case. Reviews typically take 45 days. If you accept the review conclusion, the matter is settled. If you reject it, you still have 30 days from the review conclusion to appeal to the tribunal.

What the tribunal considers

The First-tier Tribunal hears the case on the facts and law, not simply on whether HMRC followed its own procedures. For R&D claims, this typically means examining whether the company's activities meet the definition of R&D under the BEIS Guidelines on the Meaning of Research and Development for Tax Purposes. The tribunal can allow the appeal in full, dismiss it, or reach a different conclusion from both sides.

A substantial proportion of R&D tax tribunal cases turn on whether the activities involved a genuine advance in science or technology and whether there was genuine technical uncertainty. A well-prepared technical narrative, supported by contemporaneous project records, is essential for a credible tribunal case.

Re-Submitting the Claim: When It Is Possible

The time limit for making or amending an R&D tax claim is two years after the end of the accounting period to which it relates, per paragraph 83A Schedule 18 FA1998 as amended. If HMRC disallowed your claim during a compliance check and you believe the disallowance was wrong, you can amend the return to re-assert the claim, provided you are still within that two-year window.

If the original claim was simply never submitted, you can still file a new claim for any accounting period that ended less than two years ago. For a 31 March 2024 year-end, the deadline is 31 March 2026.

Re-submission is not the same as appealing. You can re-submit an amended claim whether or not you also appeal. If you amend a return to include a stronger claim after HMRC disallowed a weaker one, HMRC may accept the amended claim or open a new enquiry into it. The key is that the amended claim must be prepared more carefully than the original, with stronger technical narratives and documentary evidence.

Check out the Additional Information Form requirements to understand what HMRC now expects with every R&D submission, as this was not always required for older claims.

Switching Adviser: How It Works and What to Expect

You have the right to change your R&D adviser at any stage, including mid-enquiry. The process is straightforward. Your new adviser submits a 64-8 Authorisation form to HMRC. This replaces the previous adviser's authorisation and gives the new adviser authority to correspond with HMRC on your behalf.

There is no gap in your legal position during a change of adviser. HMRC does not pause or reset an enquiry because you changed representation. Deadlines do not move.

What you must do before the switch:

• Request a full copy of all HMRC correspondence from your current adviser, including the original enquiry opening letter, all information notices, and any representations made on your behalf.
• Obtain a copy of the original Additional Information Form submitted with the claim.
• Obtain the R&D cost schedules and technical narratives that were submitted.
• Check whether any information notice deadlines are outstanding and confirm the new adviser has capacity to respond within them.

A new adviser coming in cold needs time to understand the technical facts of your projects. Building in two to four weeks before any HMRC deadline is the minimum. If a deadline is imminent, your current adviser has a professional obligation to respond or request an extension from HMRC while the transfer takes place.

When switching adviser makes a material difference

Not every rejected claim reflects a poorly constructed one. Some HMRC disallowances follow an initial review by HMRC staff who did not fully understand the technical activities. A specialist with deep experience in your sector, such as software development, advanced manufacturing, or life sciences, can reframe the technical narrative in terms HMRC officers are trained to accept.

Equally, some claims fail at the expenditure level rather than the technical test level. If the original adviser omitted claimable cost categories, a specialist review of the qualifying expenditure categories may identify additional amounts that should have been included, which can be added in an amended re-submission.

Visit our adviser comparison guide to understand what to look for in an R&D specialist who handles enquiries, not just first-time claims.

If the Original Claim Was Submitted Without Your Knowledge

A small number of companies discover that an R&D claim was filed by an adviser without proper authorisation or contained material inaccuracies. If HMRC is now pursuing your company for repayment and penalties on a claim you did not knowingly authorise, the position is more serious.

HMRC's Compliance Handbook CH81120 deals with behaviour categories including careless and deliberate inaccuracies. If the inaccuracy was introduced by an adviser rather than the company, and the company took reasonable care, the penalty exposure may be reduced or eliminated. You should seek specialist tax investigation advice promptly rather than attempting to handle this without representation.

You should also report the adviser's conduct to their relevant professional body. HMRC-registered R&D advisers who are members of professional bodies such as the CIOT or ICAEW are subject to disciplinary processes. HMRC has also been running an Agent Strategy programme since 2023 targeting high-risk claims behaviour in the R&D adviser market.

What to Do If Your Claim Was Just Rejected

If you received a closure notice or assessment in the last 30 days, your immediate steps are:

1. Check the date on the letter and calculate the 30-day appeal deadline.
2. Request HMRC's reasons for the disallowance in writing if they are not already set out in full.
3. Obtain all submitted documents from your current adviser.
4. Decide whether you want to request an HMRC review, appeal directly to the tribunal, or both.
5. If you want a second opinion on the claim's merits, seek a specialist assessment before deciding how to proceed.

If more than 30 days have passed since the closure notice, you may still have options. The tribunal can admit late appeals in exceptional circumstances, and there may still be an amendment window open if the two-year deadline has not expired. Get a free assessment from a specialist who handles R&D enquiries to understand exactly where you stand.