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.
If convicted, Leon faces a possible maximum sentence of six years in prison.
The case is still being investigated by the Los Angeles Police Department.