Naval Academy Superintendent Vice Admiral Mike Miller has decided to charge Eric Graham with abusive sexual contact and to charge Joshua Tate with aggravated sexual assault, the school said in a statement.
Both Graham and Tate are also charged with making false official statements.
A third football player in the case, Tra'ves Bush, will not face court-martial charges, the academy said.
The three had been charged with sexually assaulting the midshipman in April 2012 at an alcohol-fueled off-campus party in Annapolis, Maryland, site of the elite school.
The allegations were among the latest in a spate of high-profile military sexual assault cases, some involving personnel whose job it was to prevent sexual abuse.
The woman faced dozens of hours of questioning during an eight-day hearing, answering many graphic questions about the party and its aftermath.