It begins in Grant County about 20 miles (32 km) northwest of Baker City near the crest of the Blue Mountains.

It flows generally west to the community of Dale on U.S. Route 395, then southwest through the city of Monument to the unincorporated community of Kimberly, where it meets the main stem of the John Day River.

[7] The North Fork John Day River is one of the most important in northeast Oregon for anadromous fish.

Wildlife found near the river includes mule deer, elk, and black bears, peregrine falcons, and bald eagles.

Recreational uses include hunting, fishing, horseback riding, hiking, snowmobiling, skiing, camping, and whitewater rafting.