The perennial stretches of the stream begin at Fossil Springs, at river mile (RM) 14 or river kilometer (RK) 23, in the Fossil Springs Wilderness of the Coconino National Forest at an elevation of about . Below the springs, the creek flows west and southwest, passing the remnants of a former dam. Unnamed intermittent streams enter from left and right. Before Fossil Creek reaches the former Irving Power Plant, it leaves the Fossil Springs Wilderness, and below the plant, it enters the Mazatzal Wilderness of the Tonto National Forest. Forest Road 708 (Fossil Creek Road) follows the creek for along this stretch, crossing the creek once at Fossil Creek Bridge.