The accused, Eric Graham, 22, faces a court-martial charge of abusive sexual contact in the case, one of a spate of sexual misconduct allegations involving the world's most powerful military.
"He will be pleading not guilty to all criminal charges," his lawyer, Chip Herrington, told Reuters after the hearing at Washington's Navy Yard. He earlier said Graham had pleaded not guilty.
Another former Academy football player, Joshua Tate, 21, faces court-martial for aggravated sexual assault, which allegedly occurred at an alcohol-fueled off-campus party in April 2012.
Tate's arraignment is scheduled for early November, according to his attorney, Jason Ehrenberg. Graham's arraignment was closed to reporters, and no date has been set for trial.
Graham, a senior, and Tate, a junior, are also charged with making false official statements. Charges against a third football player, Tra'ves Bush, 22, were dropped last week.
Naval Academy Superintendent Vice Admiral Mike Miller decided to refer the cases to courts-martial after reviewing evidence from an Article 32 hearing, held to determine if trial was warranted.
Tate's lawyers filed a motion on Tuesday to join a pending lawsuit filed in September by the female midshipman requesting that the U.S. District Court in Maryland order Miller to recuse himself from the case due to bias.
The court denied a preliminary injunction request to stop Miller from deciding whether the case should proceed to court-martial. But Tate's attorneys said the pending lawsuit could still prevent Miller from influencing jury selection.
The accuser's attorney, Susan Burke, said this week she was teaming up with another law firm, which has agreed to work pro bono on the case. Reuters does not generally report the names of sexual assault victims.
A study released in May by the Defense Department estimated that reports of unwanted sexual contact in the military, from groping to rape, rose to about 26,000 cases last year from 19,000 in 2011.
