Police say the break and enter happened just before 5 a.m. at a townhouse just south of the university on Assiniboine Road.
The intruder fled after the woman woke up and screamed, police said. She was not hurt. Police could not confirm if she attended York.
She told police the man was trying to steal her computer and got into the third floor apartment through the balcony.
Police searched the area in the York University Village, but have not made an arrest.