The vaccine, made by French company Sanofi-Aventis, will not be sold commercially, but rather stockpiled by the government if the virus H5N1 mutates into a form that is spread easily from human to human.
FDA advisers had reported to the agency in February that the vaccine was better than nothing.
The vaccine is "sort of an interim measure" until better ones are developed, said Norman Baylor, director of the FDA's Office of Vaccines Research and Review, reported Reuters. "Ideally, yes, you would like a vaccine that would have a higher efficacy."
The FDA said two injections given 28 days apart would provide "limited" protection to a pandemic. About 45 percent of the people who got the vaccine in a study developed an immune response to the virus.
The U.S. Department of Health and Human Services said it has already purchased 13 million doses of the Sanofi vaccine, which would inoculate an estimated 6.5 million people.
The vaccine was approved for people age 18 to 64. Studies in other age groups are ongoing, according to Reuters.
"The threat of an influenza pandemic is, at present, one of the most significant public health issues our nation and world faces," said FDA Commissioner Dr. Andrew von Eschenbach, the Associated Press reported. "The approval of this vaccine is an important step forward in our protection against a pandemic."
The H5N1 bird flu virus has killed 172 people out of 291 known to have been infected, according to the World Health Organization. So far the transmission has been mostly from infected birds to humans, and it remains an animal disease.
