Officials say the man raped the girl inside her home on Saturday morning.
The girl was taken to the hospital and is 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 hotel around 5 a.m. Sunday.
Authorities say there may be other victims.
Few other details were released.