Is the FAA Medical Exam an IRS Medical Expense?
If you're asking whether you can pay for one with an HSA or FSA, then yes, physical exams are eligible expenses, though consult with your insurance provider first if they are covered by your plan.

Physical Examination
You can include in medical expenses the amount you pay for an annual physical examination and diagnostic tests by a physician. You do not have to be ill at the time of the examination.

If you're looking to add it to a list of itemized deductions, as Pondlife explained, it generally has to be business- or workplace related.  If you are a professional pilot, then this is deductible.

What Can I Deduct?
To be deductible, a business expense must be both ordinary and necessary. An ordinary expense is one that is common and accepted in your industry. A necessary expense is one that is helpful and appropriate for your trade or business. An expense does not have to be indispensable to be considered necessary.