The call came in at 12:28 p.m. near Scrabble Road in the area of Dam 4 in Shepherdstown.
Rescue crews say witnesses heard screams, and saw the 64-year-old victim pinned under a tractor.
Crews were able to free the man at 1:18 p.m. Thursday. They say he suffered traumatic injuries to his lower extremities.
The man was flown to Winchester Medical Center for treatment.
Shepherdstown Fire Department medics and Jefferson County EMS assisted on the scene.