The FAA has statutory authority to deny medical certificate applications. They exercise this authority using the medical standards set forth in 14 CFR Part 67. There are two distinct options available to pilots who wish to question and/or dispute a medical denial: FAA reconsideration and NTSB review.
14 CFR 67.409(a) establishes that a person may seek reconsideration within 30 days of a denial by an aviation medical examiner. However, AME’s are designees of the FAA and rarely deny applications; instead, they defer the decision to the FAA. So, more commonly, it’s the federal air surgeon, a regional flight surgeon, or the manager of aeromedical certification division that denies a medical application by sending you a letter telling you the reason for the denial. Practically speaking, reconsideration is available regardless of who does the denying. In seeking reconsideration, a person is asking the FAA to re-review the denial and to reassess the person’s eligibility for medical certification. The request for reconsideration must be made in writing and should normally include medical information in support of the request, such as doctor statements, test results, etc. In reviewing the request, the FAA also may consider the person’s eligibility for a special issuance medical certificate (authorization). If the FAA is unpersuaded by the request, they will issue another letter confirming the denial.
A final denial by the administrator may be appealed to the National Transportation Safety Board. More accurately, an airman may file with the NTSB a petition for review of the administrator’s denial, often referred to as an appeal. It’s notable that the referenced “Administrator” includes the federal air surgeon, the manager of aeromedical certification division, and regional flight surgeons, but does not include an aviation medical examiner. In other words, an AME’s denial is not considered a final denial by the FAA. The petition must be filed within 60 days of the denial, and it basically constitutes a request for a hearing with an NTSB law judge. At the hearing, the petitioner and the FAA will both present evidence and expert testimony to support their positions and the law judge will make “findings and conclusions upon all material issues of fact, credibility of witnesses, law and discretion presented on the record.” In the end, it’s often an uphill battle for the petitioner, as he or she has the burden of proving eligibility for medical certification.