Police say the minivan was parked outside a hotel with its hazard lights flashing. It's not clear how long it had been there.
Officers with a dog investigated the vehicle and then moved it to the side of the street.
Police had closed a few blocks around the area, including 43rd Street from Eighth Avenue to Times Square, but later reopened them.
The central area of Times Square most frequented by visitors was not evacuated and was filled with taxis and tourists as usual during the incident.