The Marathon County Comprehensive Plan 2006 was adopted unanimously in its entirety by the Marathon County Board of Supervisors on May 23, 2006. The plan is now part of the General Code of Ordinances for Marathon County, Chapter 26.

Marathon County's comprehensive planning process includes the development of 50 individual municipal comprehensive plans and a County Development Plan. The municipal plans cover issues and proposals specific to that community. The County Plan includes the future land use maps of the individual municipal plans, but also addresses regional issues such as transportation, environment, etc. The County Plan addresses factors that cross municipal boundaries and affect the county as a whole.