The Middle Fork John Day River is a 73-mile (117 km) tributary of the North Fork John Day River in the U.S. state of Oregon.

It originates in the Blue Mountains of northeast Oregon in the Malheur National Forest near Austin and flows generally west to the North Fork about 18 miles (29 km) above Monument.

The Middle Fork drainage basin covers about 806 square miles (2,090 km2).

[4] The Oregon Scenic Waterways Program, administered by the Oregon Parks and Recreation Department (OPRD), protects the river for most of its length.

People planning to cut trees, mine, build roads or structures, or make other substantial changes within 1⁄4 mile (0.40 km) of the river must first notify OPRD and seek its approval.