The crash happened around 4:56 p.m. at West 51st Street and South Wentworth Avenue, ISP officials said.
State police said the trooper was driving northbound on Wentworth when someone ran a red light and hit the trooper's vehicle.
The trooper was taken to a local hospital with injuries, ISP said. Their squad vehicle was damaged and towed from the scene.
There was no word yet on any charges as authorities continue to investigate.