Lakesite operates under a Manager-Commission charter. The Commission is made up of five members, elected at-large for four-year terms. Elections are staggered so that terms overlap. After each election, the Commission elects a Mayor and Vice-Mayor from among its members. In addition, Commissioners are appointed to chair committees to oversee the business of the city. Current committees include Public Safety, Budget and Finance, Parks and Recreation, and Public Works.
The commission appoints a City Manager who is responsible for conducting the day-to-day affairs of the city under the direction of the commission. The City Manager appoints and oversees the work of other city personnel.