The Altra Top of Utah Marathon starts at Hardware Ranch, in the Wasatch Mountains southeast of Logan, Utah. Hardware Ranch is a wildlife management area where wild elk are fed during the winter to keep them from roaming into Cache Valley, where Logan is located. From Hardware, the race winds down Blacksmith Fork Canyon, passing river banks, marshes, limestone outcroppings, fall foliage, and cool canyon vistas. Moose, elk, deer, and many other species of wildlife make the canyon their home.
Reaching Cache Valley at mile 14, the course follows mostly side roads through the small communities of Nibley, Millville, Providence, and River Heights before ending at Merlin Olsen Park, in Logan. Before the race, runners are bused from the park to the start line. The course is USAT&F-certified, which means it can be used to qualify for the Boston Marathon, and it has a net elevation drop of 1,045 ft.