The Stadtmuseum is a cultural institution supported by the local community of Rapperswil-Jona as well as the city (political municipality). Both municipalities contributed an equal share of the costs for the 2010/12 renovation and jointly finance the ongoing operations. The institution is overseen by the local community as the owner of the property (Museum Department).
The Museum Advisory Board is responsible for the strategic orientation of the Stadtmuseum. This committee is chaired by the head of the Museum Department of the local council. The Museum Advisory Board is made up of two representatives from the local community and the city, four experts and the Museum Director in an advisory capacity. The latter is responsible for managing the museum in matters of operations and content.