The City of Monticello has a Mayor-Aldermanic form of government. The city council is the governing body of the city elected by the public, and the City Administrator is hired by council to carry out the policies it establishes.

The City Administrator is responsible for preparing the budget, directing day-to-day operations, and personnel management.

The City is organized into departments, each managed by a professional in their particular field, who reports to the City Administrator.