The Wild Rice River rises in Sargent County in southeastern North Dakota near the town of Bramton about 75 miles southwest of Fargo.

The river flows easterly into Lake Tewaukon and then exits the lake's north side flowing by Cayuga turning northeasterly and then east through Mantador and Great Bend. It then heads north going by Dwight, Galchutt, Abercrombie, Christine, Hickson, Oxbow, the town of Wild Rice, Briarwood, and Frontier before emptying into the Red River of the North at Fargo.

Tributaries of the river include its South Branch, the White Earth River, Marsh Creek, Felton Ditch, Moccasin Creek, Spring Creek, Mashaug Creek and Coon Creek.