Waubun is a city in Mahnomen County, Minnesota, United States.

When the Soo Line was built through the county in 1903–4, the general manager, Pennington, and his chief engineer, Thomas Green, named the stations as they moved the line north; all towns on the reservation had to have Native American names.

The community post office was established in 1905 as Bement and changed to Waubun in 1906.

[6] Waubun is in southwestern Mahnomen County on the west side of U.S. Route 59, which leads north 10 miles (16 km) to Mahnomen, the county seat, and south 5 miles (8 km) to Ogema.

State Highway 113 runs along the community's south side, leading east 20 miles (32 km) to Elbow Lake and west 15 miles (24 km) to its terminus at Syre.

According to the U.S. Census Bureau, Waubun has an area of 0.51 square miles (1.32 km2), all of it land.

The racial makeup of the city was 66.75% White, 17.12% Native American, and 16.13% from two or more races.