In a complaint filed Friday, the woman, now 22, says she was raped on separate occasions by two different midshipmen. After she reported the assaults to an academy counselor, she says, the academy forced her to drop out.
"Both institutions systematically and repeatedly ignore rampant sexual harassment," they say in the complaint filed in U.S. District Court in New York. "Both institutions have a history of failing to prosecute and punish those students found to have sexually assaulted and raped their fellow students."
A spokesman for the Naval Academy declined to comment on the lawsuit but said the institution takes every report of potential sexual harassment or assault "extremely seriously."
Cmdr. William Marks, the academy spokesman, said the school's sexual assault response program "is among the strongest in the nation." Each report is "thoroughly investigated," the results are reviewed by legal experts and "appropriate action taken whenever the evidence allows us to do so," he said in a statement.
Marks said students who report assault or harassment are offered physical and psychological counseling for as long as they want, even if it extends beyond their time at the academy. He said the academy's sexual assault response coordinator, a Navy commander, reviews every case.
The women are seeking unspecified monetary damages. They name former Defense Secretary Robert Gates and former Naval Academy Superintendent Vice Adm. Jeffrey L. Fowler among the defendants.
The Baltimore Sun does not identify alleged victims of sexual assaults.
The former midshipman, a varsity soccer player, entered the Naval Academy in 2008. She says she was raped by a fellow midshipman after falling asleep at a drinking party that fall, and again by a different midshipman several months later after drinking and passing out in a hotel room away from the Annapolis campus.
She says she spoke of the assaults to an academy counselor, but the counselor did not encourage her to report them to civilian or military law enforcement. She says she experienced symptoms of post-traumatic stress disorder and became suicidal.
Ultimately, she says, she reported the assaults to the academy. She says the academy concluded that her mental health issues precluded her from being commissioned as an officer, and forced her to drop out before she could earn her degree.
The lawsuit came days after Defense Secretary Leon E. Panetta announced new steps to combat sexual assaults involving service members.
"Sexual assault has no place in the military," he told reporters Monday after a closed-door meeting with members of the House Armed Services Committee. "It is a violation of everything that the U.S. military stands for."
Panetta said he would issue a directive to change the way allegations are handled, with the most serious offenses subject to court-martial review at the level of a Navy captain or an Army colonel, ensuring that cases would remain within the chain of the command and leaders would be held accountable.
Panetta also said he would work with lawmakers on creating special victims units within the services, allowing National Guard and reserve members to remain on active duty after filing a complaint, and ensuring that service members receive an explanation of sexual assault policies within 14 days of entering the military.
Panetta also spoke of steps the Defense Department already has taken, including the creation of a 24/7 telephone hot line and the appointment of a two-star general to head the Pentagon's Sexual Assault Prevention and Response Office.
The Defense Department said last week that the number of sexual assaults involving service members reported in fiscal year 2011 increased by 1 percent to 3,192 cases.
But the Pentagon has also estimated that 86 percent of sexual assaults go unreported. Victims have expressed concerns about the judicial process and the impact of reporting on their military careers.
At the Naval Academy, reports of sexual assaults doubled last year to 22, officials said in December. It was the fourth straight year the number had increased.
It is unclear whether the trend reflects a growing number of assaults or a greater willingness of victims to report them.
The Associated Press contributed to this article.