Joseph McCain was being held without bail in Orange County pending extradition proceedings, Acting Bergen County Prosecutor Gurbir S. Grewal said.
He is charged in New Jersey with aggravated sexual assault and child endangerment.
Authorities tracked down McCain, who is married, and arrested him at his Orlando home on Thursday, the prosecutor said.
The search began on Jan. 29, after Grewal's office received a telephone call from the Pennsylvania State Police barracks in Blooming Grove about the alleged rape.
Detectives from the prosecutor's Special Victims Unit interviewed the alleged victim, who Grewal said "provided specific detail regarding acts committed upon her" by McCain.
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