The NYPD arrested the girls' father, 24-year-old Robert Byrne, in Manhattan's West Side on Friday afternoon.
He was in a vehicle, police say, and managed to run into a building before being caught.
Authorities say the girl, Ava Byrne, appeared to be okay, but was still taken to the hospital to be checked out.
She had been reported missing from Luzerne County.
Police say a civilian recognized the car. That person flagged down a traffic agent, who then notified police.
Officers pulled the vehicle over and took Byrne into custody without incident.