A nurse was said to have walked in on Keith Nembhard, 37, while he was sexually assaulting the woman.
Officials at Bronx-Lebanon Hospital called security straight away and the suspect was held until police arrived.
Officers ultimately charged him with second degree rape.
Nembhard allegedly knew the victim, who is 32, but doctors said the patient’s injuries meant she was unable to consent to sexual intercourse.
The incident happened earlier this month and police released details about it yesterday.
Bronx-Lebanon Hospital was at the centre of another serious incident in June when Dr. Henry Bollo shot dead a colleague and injured six others after going on a shooting spree.
He then shot himself dead.