Police say Colin Kennedy, 18, attacked the women on January 13 and 14 at Fordham Hall, a dormitory in the 6400-block of North Sheridan Road.
Kennedy, who is a freshman student majoring in international business, now faces criminal sexual assault charges.
He appeared in court Tuesday morning and is being held on a $300,000 bond.
Prosecutors allege he told the women he needed a place to sleep. Once he was in their rooms, they say he forced himself on them.
Kennedy's attorney says he denies any wrongdoing.
Meanwhile, some Loyola students said they were unaware of the alleged incidents.
"I think it's really horrible. That's so sad. How could somebody do that?" said a student.
"It's really frightening. I would hope that we would be a little more respectful to each other as students and peers. But you just have to be aware of your surroundings and know what's going on," said another student.
Loyola is now offering a new 24-hour misconduct hotline. Students can access the confidential EthicsLine online or by calling (855) 603-6988.