"He told me when she was out of town that he'd felt a lump in her breast and needed to feel my breasts because he didn't want to upset her, but he needed to feel mine," DeGeneres said.
DeGeneres said the man also attempted to break into her room and that she fled out the window.
She said she never told her mother because she "was protecting her and I knew that would ruin her happiness."
The comic said she's now angry at herself because she didn't stand up to her attacker, even though she was only 15 or 16 at the time.
"It's a really horrible, story and the only reason I'm actually going to go into detail about it is because I want other girls to not ever let someone do that," she told host David Letterman.
The Ellen Show host added that she hid the assault from her mother for a few years, and when she did tell her, she didn't believe her "and then stayed with [her husband] for 18 more years."
DeGeneres said that finally, Betty DeGeneres left her husband "because he'd changed the story so many times."
She hopes her story helps other victims of sexual assault come forward. "We [women] just don't feel like we're worthy, or we're scared to have a voice, and we're scared to say no," she says.
"That's the only reason I think it's important to talk about it because there's so many young girls and it doesn't matter how old you are. When I see people speaking out, especially now, it angers me when victims aren't believed, because we just don't make stuff up. And I like men, but there are so many men that get away with so much."