The ban was put in place at the start of the Aids crisis during the 1980s.
Groups that handle blood donations lobbied for the change, calling the ban on gay donors "medically unwarranted".
While calling the decision a "step in the right direction", activist David Stacy said the FDA needs to go further.
"It continues to stigmatize gay and bisexual men," said Mr Stacy, a spokesman the Human Rights Campaign. "It simply cannot be justified in light of current scientific research and updated blood screening technology."
Blood donation around the world
-UK (excluding Northern Ireland), Japan and Australia have a one-year ban on men who have had sex with other men
-Canada has a five-year ban
-No ban in Italy, Mexico, Poland, Portugal, Russia and Spain, but some of those countries have tougher screening questions
Why are blood donors asked their sexual history?
The FDA`s decision follows a formal recommendation in 2014. The federal agency sets national standards for blood donations, which are tested for diseases.
Before the rule change, potential donors in the US who admitted having sex with other men after 1977 were not allowed to give blood.
The new policy treats gay men the same as other higher risk groups. People who have sex with prostitutes or have used intravenous drugs in the past 12 months are also barred from giving blood.
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