The Skaneateles Turnpike began at the Cherry Valley Turnpike in the hamlet of Clintonville, that at that time had a tavern and a large barn for the stagecoach horses, located about 4 miles (6.4 km) east of the village of Skaneateles in western Onondaga County.
From Tully, the road took on a slightly northeasterly alignment for 20 miles (32 km), passing through Fabius, New Woodstock, and Erieville on its way to Eaton.
The remaining 25 miles (40 km) of the turnpike served only a handful of small hamlets, scattered across sparsely populated areas of modern Madison and Otsego counties.
The largest of these were Brookfield in eastern Madison County and Leonardsville, a riverside community located just south of where the road crossed the Unadilla River.
[1] In 1807 the company was authorized to intersect the Great Western Turnpike (now U.S. Route 20) at any point east of the west branch of the Unadilla River.