The state highway runs 59.17 miles (95.22 km) from the West Virginia state line near Mountain Grove, where the highway continues as West Virginia Route 39 (WV 39), east to U.S. Route 11 (US 11) in East Lexington.

SR 39 begins at Ryder Gap at the West Virginia state line, which also serves as the boundary between George Washington National Forest and Monongahela National Forest and between the James River and Monongahela River watersheds.

SR 39 ascends the east side of the mountain along O'Rourke Draft, then descends to the Jackson River.

SR 39 has a short concurrency with US 220 (Ingalls Boulevard) north of the village in which the highways pass the Jefferson Pools.

SR 39 and SR 42 leave the Cowpasture River and enter the valley of Mill Creek, which the highways and a CSX rail line follow through the gap in Mill Mountain at which they enter Rockbridge County and the town of Goshen and continue as Maury River Road.

[1][2] South of Goshen, SR 39 leaves the rail line after an at-grade crossing and follows the Calfpasture River through a gap between Bratton Mountain and Knob Mountain and passes to the south of Lake Merriweather, an impoundment of the Little Calfpasture River.

East of the gorge, the state highway crosses to the north side of the river and passes through Rockbridge Baths.