The route proceeds north from its southern terminus along the shore of Lake Seminole in southern Seminole County to a point just southwest of Omaha, where it travels in an easterly direction until it meets its northern terminus, an intersection with US 27/SR 1 in a rural south of the unincorporated community of Louvale.

It then turns to the north and skirts along the western edge of the park, intersecting SR 253 (Bainbridge Highway) on its northwestern corner.

In Donalsonville proper, adjacent to Davis Park, is an intersection with SR 91 (Marianna Highway).

Less than 500 feet (150 m) after crossing over a CSX railway line, the two routes diverge, with SR 39 heading northwest on West Crawford Street.

About 1 mile (1.6 km) north-northwest of the county line, SR 39 curves to a due north routing.

In Jones Crossroads is an intersection with SR 273 (Papermill Highway).. After curving to the north-northeast, the route enters Lucile, where it has a short segment on the Early–Miller county line.

On the way, they pass east of Blakely Cemetery and intersect SR 62 (Columbia Street), which joins the concurrency.

At the intersection with Fort Gaines Street, SR 39 departs to the northwest and leaves the city.

North of Fort Gaines, SR 39 intersects the western terminus of SR 266 (Coleman Road) and runs along the eastern shore of Walter F. George Lake, and passes just east of George T. Bagby State Park.

Then, SR 39 departs to the north-northeast, running parallel to the Chattahoochee River and entering Stewart County.

Just southwest of Omaha, the route intersects the eastern terminus of SR 39 Spur and makes a nearly 90-degree turn to the east.

After crossing over a CSX railway line, it continues to the east until it meets its northern terminus, an intersection with US 27/SR 1 in a rural area south of the unincorporated community of Louvale.