Officials say the man raped the girl inside her home in Brownsville on Saturday morning.
The girl was taken to the hospital and was said to be stable.
The 45-year-old suspect, identified as Andre Clark, is facing three counts of rape, sexual abuse and acting in a manner injurious to a child. He was found in a Queens hotel around 5 a.m. Sunday.
Authorities say there may be other victims.
Police could not provide any further details at this time.