The South Fork John Day River is a 60-mile (97 km) tributary of the John Day River in the U.S. state of Oregon.

It begins in the Malheur National Forest in Harney County about 25 miles (40 km) north-northwest of Burns and flows generally north to Dayville, where it meets the main stem of the John Day River.

Along the way, the stream passes through the abandoned town of Izee.

The Black Canyon Wilderness in the Ochoco National Forest lies within the river's drainage basin.

[6] A total of 47 miles (76 km) of the river, from the Malheur National Forest boundary to Smoky Creek, are classified "recreational" in the National Wild and Scenic River (NWSR) system, created under the Wild and Scenic Rivers Act of 1968, and offer opportunities for hiking, swimming, camping, hunting, and fishing.