Cordrea Brittingham and Arion Keith Williams, both were charged with second-degree rape, a felony punishable by up to 30 years in prison. They were held on $250,000 bond each.
Brittingham and Williams also were charged with second-degree sex offense, a non-consensual sex act punishable by up to 20 years in prison. Williams also was charged with third-degree sex offense, non-consensual sexual contact punishable by up to 10 years.
The alleged assault occurred late Thursday or early Friday.
The woman said she had become intoxicated and passed out in a bedroom. When she awoke, she found herself being assaulted, police said. She said she pushed the two men away, and they left the home.
Brittingham, 21, of Berlin, Md., and Williams, 21, of Detroit, were on the Navy football team last season, during their sophomore year.
Anne Arundel County Police took custody of the two midshipmen Monday afternoon, said Officer Tom O'Connor. They were turned over to the county's criminal investigation unit in Crownsville by Naval Intelligence.
Academy spokesman Cmdr. Mike Brady would not comment beyond reading a statement saying two midshipmen had been charged.
The Naval Academy has been rocked in recent years by a series of scandals involving drug use, car thefts and sexual assaults on female midshipmen.
Several midshipmen have been expelled for sexual misconduct or fraternization.