Jose Ramos faced a judge for the first time Wednesday night. He is accused of carrying out the crime Sunday night inside an apartment on West 174th Street.
He is charged with second-degree and first-degree rape, sexual abuse and endangering the welfare of a child.
Police sources previously told News 12 that the victim was watching movies with Ramos prior to the assault, which they say took place between 10:30 p.m. and 3 a.m.
The nature of the relationship between Ramos and the victim remains under investigation.
Sources say he has no previous criminal history.
Ramos' bail was set at $50,000 cash/$100,000 bond.
He is due back in court Friday.