Mt. Vernon is located in the center of the John Day Valley in Grant County, Oregon. Its post office was established in 1877 and named after a black stallion that belonged to settler David W. Jenkins. The stallion's stable, a small stone building, is still standing in a field on the north side of U.S. Highway 26 about 2.2 miles (3.5 km) east of the main intersection in town.
The city has a total area of 0.68 square miles (1.76 km²), all land.  It is located along  U.S. Route 26 on the John Day River about 8 miles (13 km) west of the city of John Day.