The City of Joseph was named the interim county seat until a general election chose Enterprise as the county seat in 1888. A proposition to contribute to the building of a county courthouse by sixty citizens was turned down by the county court in 1899. It was not until 1909 that a courthouse was built. Constructed of native stone the building continues to house county offices. Enterprise, in addition to being the county seat, is the Wallowa Valley's trade center for ranchers and headquarters for the Wallowa National Forest.
County government consists of a county court made up of a county judge and two commissioners.
Other offices include clerk, sheriff, assessor, treasurer, and surveyor. The county is served by Senate District 29, Representative District 58, and the Second Congressional District. Principal industries in Wallowa County are agriculture, livestock, lumber, and recreation.