The highway connects various rural communities and towns from the southwest to the northwest sections of the state.

SC 39 is a two-lane rural highway that travels 100.7 miles (162.1 km) from the Savannah River Site to U.S. Route 221 (US 221) south of Laurens.

By 1942, SC 39 reached its apex with an extension into Millett, giving it a length of over 145 miles (233 km).

Also, during the same period, SC 39 was truncated to its current southern terminus at the Savannah River Site boundary near a realigned routing of SC 28 (today's US 278); a majority of its former route now within the Savannah River Site still exists, though sections have been removed or submerged under Par Pond.

It travels to the north-northwest and curves to the north before it reaches its northern terminus, an intersection with SC 391 (Wire Road).