Wisconsin Department of Transportation (WisDOT) policy prohibited dual designations within the state trunk highway system, prior to the commissioning of Interstate 39 (I-39) in 1992.

WIS 39 begins at the intersection of US Highway 18, less than a quarter of a mile (roughly 200 meters) from the unincorporated community of Edmund, Wisconsin.

In the center of Linden, WIS 39 heads southeast on Main Street out of town, through the hills of Southwestern Wisconsin, crossing under US Highway 151 outside of Mineral Point.

The two state highways turn southeast on Doty Street just northeast of the downtown area to head out of the city.

After crossing the Sugar River State Bike Trail (built on a former railway line), the route ends at its eastern terminus of WIS 69.

Since 1999, the connection to Albany was degraded to County Highway F in accordance to transferring part of it (Monticello–Albany) back to local control.