Boise City has a strong mayor-council form of government. The Mayor works full-time, managing the day-to-day operations of the City and providing leadership and policy direction to the City Council. The Mayor chairs all meetings of the City Council, voting only in the case of a tie. The six members of the City Council work part-time, holding budget and policy-setting authority for the City.

The Mayor and City Council members are elected at large by popular vote. City Council members are elected to a specific Council seat, but the seats are not determined geographically.