The byway forms a loop in southwestern Colorado traversing the heart of the San Juan Mountains.

The San Juan Skyway reaches its zenith at Red Mountain Pass at elevation 11,018 feet (3,358 m).

Starting in Durango, Colorado, the largest city on San Juan Skyway, the byway follows U.S. Highway 160 (US 160) west through the town of Mancos to Cortez passing the entrance to Mesa Verde National Park.

From Rico the byway crosses 10,222 ft (3116 m) Lizard Head Pass and enters the Uncompahgre National Forest.

The Alpine Loop National Back Country Byway, a four wheel drive jeep road, takes off in the gorge south of Bear Creek Falls.

At this point the byway enters Ironton Park, a nice flat valley in contrast to the gorge.

Back into the San Juan National Forest the highway descends through the Chattanooga Valley to Silverton.