But jurors convicted Lamar S. Owens Jr. on charges of conduct unbecoming an officer and disobeying a lawful order.
"They have determined, obviously, that the consensual act took place," said Cmdr. John Maksym, the trial judge. He added that the jury of five Naval officers found that Owens "wrongfully entered the room without permission and wrongfully engaged in consensual sex."
Owens, standing at attention as the verdicts were read, showed no emotion. He remains free without bond. He was not allowed to graduate or receive a commission in May, and remains a midshipman.
Neither Owens' accuser nor her family were in court when the verdict was read.
The trial's punishment phase will begin Friday morning. Prosecutors recommended a sentence of two years on the conduct unbecoming an officer charge. The judge tabled discussion of a sentence on the other charge until Friday.
Maksym also said he would consider whether to set aside either of the charges. During the trial, the judge chastised prosecutors for what he called "the anemic nature" of their witnesses.
He was especially critical of the qualifications of expert witnesses prosecutors called to rebut questions raised by Owens' attorneys about why the woman didn't cry out that night and didn't immediately notify authorities.
"Everyone's reaction is relief," said Reid Weingarten, Owens' civilian defense counsel. "There is no evidence that Lamar Owens raped this woman."
He was also optimistic that the other charges would eventually be set aside.
"We're very confident that conduct unbecoming will go," he said. "There was no evidence presented at trial to support that charge. ... The accuser offered no recollection of the events and Owens said that he was invited."
The conviction for failure to obey a lawful order stemmed from Owens' violation of a Naval protective order aimed at keeping him away from his accuser's room.
Of that charge, Weingarten said: "Lamar Owens was in the wrong hall at the wrong time. Owens had no intention of harassing his accuser and had spoken to others about leaving her alone."
Owens, 22, of Savannah, Ga., was charged after an incident in the room of a female midshipman at the academy's Bancroft Hall on Jan. 29. Owens testified that the sexual encounter was consensual; his accuser testified that she repeatedly rejected his advances.
Both Owens and his accuser testified that they had several drinks at separate locations in Baltimore and Annapolis in the hours before their early morning encounter.
Other witnesses said the young woman was seen having as many as nine drinks at a restaurant and later at an Annapolis bar favored by midshipmen.
Owens was a team captain and starting quarterback for Navy last season, leading the team to an 8-4 record with victories over Army and Air Force, and a win over Colorado State in the Poinsettia Bowl.