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The voters of the City of Eau Claire adopted a City Manager form of Government in 1949, and Eau Claire has been operating under that system since. It combines the political leadership of elected officials with the professional managerial experience of a City Manager. Approximately 60 percent of the cities in the United States with a population of 25,000 or more have an appointed local government manager.

Wisconsin Statutes Chapter 64, Subchapter 1, describes the powers of the City Council and the City Manager under the this form of government. It provides that the City Council is the legislative body and exercises legislative and general ordinance powers for the City. The City Manager is the chief executive officer and exercises executive and general administrative powers for the City. The organization of the City government is further defined under Chapters 2.04 and 2.08 of the City of Eau Claire Code of Ordinances.

In November of 1992, the voters of Eau Claire passed a referendum specifying the election of a City Council president at-large, with five Council members elected from five aldermanic districts and five Council members elected at-large. Eau Claire is the only city in the state of Wisconsin to have a City Council president elected directly by the voters.