Similar to other Idaho counties, an elected three-member county commission heads the county government. Other elected officials include clerk, treasurer, sheriff, assessor, coroner, and prosecutor.
With a strongly conservative population, Madison County is one of the most staunchly Republican counties in the United States. Since 1980 no Republican presidential candidate has failed to carry the county with less than 59 percent of the vote. In that same period Republican presidential candidates polled more than 90 percent of the county's vote on two occasions, Ronald Reagan in 1984 and George W. Bush in 2004. John McCain came close to this level in 2008, drawing 85 percent of the vote.
At the state level Madison County is located in Legislative District 34, which currently has an all-Republican delegation in the Idaho Legislature.