The Piper PA-38-112 Tomahawk went down south of downtown Peterborough on the shores of Lake Ontario at 1:20 AM local time.
Images of the wreck showed a crushed nose and cockpit, and broken wings.
Peterborough police inspector Lynne Buehler told a press conference the man appeared to have been "attempting to land the plane."
He was pronounced dead at the scene. It was unclear if he was licenced to fly or had any cockpit experience.
The aircraft was reported stolen from a rural airstrip near Markham, Ontario, about 100 kilometers west of the crash site, said York Regional Police, which has taken over the investigation.