Some gay activists called the one-year rule discriminatory, but it matches policies in other counties including the UK, Australia and Japan.
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 for the Human Rights Campaign. "It simply cannot be justified in light of current scientific research and updated blood screening technology."
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.
The US Food and Drug Administration (FDA) will allow gay men to donate blood if they have been celibate for one year - lifting a 30-year ban.