Eduardo Leon, 27, has been charged with stalking, first-degree residential burglary, vandalism and resisting arrest.
Rihanna was not home at the time of the alleged incident in Los Angeles on 9 May.
Leon, from Fullerton, California, is due to appear at the Foltz Criminal Justice Centre on Monday.
The suspect is accused of hopping a fence and entering a house owned by Rihanna in the Hollywood Hills.
He allegedly spent 12 hours inside the home and was arrested the next day after being discovered by the singer's assistant.