Fresno police say it happened around 3 am at an apartment complex on Huntington Boulevard near Highway 41 in central Fresno.
Investigators say the woman woke up to a man in her room. She told police he threatened her with a gun and then left out her bedroom sliding glass door.
Police believe the man also entered her apartment through that sliding door.
There is no description of the suspect.
Officers say nothing was taken from the apartment.