In addition to including men in the definition of rape, the Obama administration also dropped the requirement that victims must have physically resisted their attackers.
Supporters say the change will give law enforcement more accurate information about fighting crime.
The new definition will up the number of people counted as rape victims in FBI statistics, but it will not change federal or state laws or alter charges or prosecutions.
The expansion of the definition has been long awaited because policymakers and lawmakers use crime statistics to allocate resources for prevention and victim assistance.
Since 1929, the FBI has defined rape as the carnal knowledge of a female, forcibly and against her will.
The new definition includes any gender of victim or attacker and covers instances in which the victim is incapable of giving consent because of the influence of drugs or alcohol or because of age. Physical resistance is not required.
The Justice Department said the new definition mirrors the majority of state rape statutes now on the books.
Nearly 1 in 5 women and 1 in 71 men in the U.S. have been raped at some time in their lives, according to a 2010 survey by the National Center for Injury Prevention and Control of the Centers for Disease Control and Prevention, which used a broader definition.
The revised FBI definition says that rape is "the penetration, no matter how slight, of the vagina or anus with any body part or object," without the consent of the victim. Also constituting rape under the new definition is "oral penetration by a sex organ of another person" without consent.
The Associated Press contributed to this report.
