The southern terminus of the highway is at its intersection with U.S. Route 11 (US 11) near Livingston.

The northern terminus of the highway is at its intersection with SR 14 at Clinton, an unincorporated community in western Greene County.

SR 39 is a rural, two-lane highway that serves as a connecting route between Livingston and western Greene County.

From its southern terminus at US 11, the highway travels in a northerly direction.

From Gainesville, the highway turns to the northeast, continuing this trajectory until it intersects SR 14 at Clinton.