Wells County is governed by a board of five County Commissioners elected for four year terms. Each Commissioner represents a population district of the County which is determined by census figures. Commissioners must live within their district; however, they are elected by the County as a whole.

The Commissioners set policies regulating the functions of the county departments and oversee the financial affairs of the County. Responsibilities of the board include establishing voting precincts, levying taxes, making appropriations, authorizing bonds, setting salaries, approving bills, accepting bids, and approving the annual county budget, along with various other duties. The Board also acts as the County Board of Equalization to review and approve property assessments.

The Wells County Commissioners meet on the first Tuesday of each month.