The agency said the possible side effects, such as drowsiness, of taking medications like Prozac do not pose a safety hazard.
The ban had affected as many as 10,000 pilots. It was lifted at the urging of unions representing aircraft owners, pilots and crews. The FAA said its own research led to a better understanding of depression and medications to treat the condition.
The new policy takes effect next Monday. Under the change, pilots can get the government's permission to take one of four drugs, known as Prozac, Zoloft, Celexa and Lexapro. The antidepressants are classified as SSRIs, which help regulate mood.
