The City of Shawnee is a city of the 1st class. As such, it has the authority of home rule, which allows cities to determine many policy issues on their own. Shawnee's charter form of government is the Mayor-Council-Manager form, which vests the policy making authority in the City Council with veto power given to the Mayor. The City Manager makes all administrative and personnel decisions regarding the implementation of council policy. The role of the manager is to provide professional knowledge of all areas of municipal government and advice on accepted public administration practices.

The Mayor is the titular head of the city and presides at all council meetings. He or she signs all ordinances and resolutions passed by the council and can veto any ordinance or resolution except for charter ordinances. An ordinance or resolution vetoed by the Mayor may be overridden by a 3/4 vote of the council. The Mayor also signs all contracts authorized by the governing body before the city is liable. The Mayor represents the governing body at official city functions. The Mayor may make recommendations to the council concerning city policies, practices, or activities, but can not make a motion. After every regular city election, the council elects one of its members as Council president, who in the absence or disability of the Mayor, becomes acting Mayor. When there is a vacancy in the office of Mayor, the Council president becomes Mayor until a Mayor has been elected for an unexpired or full term.

The role of the councilmember encompasses a broad range of activities with the level of participation being established individually by each councilmember. Some councilmembers view their role as that of ombudsmen and focus primarily on constituency services, acting as a conduit between their constituency and the city administration. Other councilmembers view their role as that of a community leader who promotes the welfare and development of Shawnee. The Municipal Code charges all councilmembers with the role of policy maker. Collectively, the council determines what the city is or wants to be and determines the direction to take to achieve a constantly redefined goal. Formal policies include city ordinances and resolutions as well as written administrative policies. Most city ordinances are codified into a Municipal Code, with some exceptions, most notably zoning and franchise ordinances. If a vacancy in the office of a councilmember occurs from January 1 to May 1 of any year, the remaining Council Members present and voting, may act to fill the vacancy until the annual Fall election of such year. If a vacancy in the office of a councilmember occurs from May 2 to December 31 of any year, the remaining Council Members present and voting, may act to fill the vacancy until the completion of a special election called as provided by law.

The City Manager is responsible for the administration of the city's affairs. He or she has the power to appoint and remove all department heads and officers. The City Manager is charged with seeing that all laws and ordinances are enforced. He also makes recommendations to the governing body in all matters concerning the welfare of the city and has a seat, but no vote in all the public meetings of the governing body. The City Manager is responsible for preparing and presenting the annual budget to the governing body and keeping the city council fully advised as the financial conditions and needs of the city. He or she is appointed by the governing body and holds office at the pleasure of the governing body.