The seven-year-old victim was visiting the fourth-floor theater complex with her father and younger sibling. The girl's father waited nearby in the concession while she used the women's restroom.
The victim was in the bathroom for less than three minutes when, police said, Elio Pintado of Summit, who had entered before her, assaulted the child in a stall.
Investigators said Pintado, who had pulled-up his collar as he entered the women's bathroom, was captured on surveillance video exiting the restroom seconds before the girl returned to her father.
Pintado was being held at the Union County Jail in Elizabeth, New Jersey. He was arrested last week for allegedly trying to lure a child into a car. He was ordered held without bail because of a parole violation, said Union County Prosecutor Theodore J. Romankow.
Authorities said two women in New Jersey made the connection to the West Nyack case after seeing the man on theater surveillance video.
Clarkstown police said search warrants led to evidence and the charges in New York.
Pintado's arraignment is pending.
He faces up to seven years in state prison if convicted.