The San Manuel Band of Mission Indians, a sovereign tribal nation, operates under its own system of government and ordinances. The tribal government provides political and economic security to its people and works to develop and maintain mutually beneficial relationships with the United States and other governments, while working within federal guidelines.

The San Manuel Band of Mission Indians governmental system is comprised of two bodies: the General Council and Business Committee. The General Council is the legislative body that acts as the tribe's governing council. The Business Committee is a seven-member body that oversees the day-to-day operations.

The Business Committee's principle function is to handle the daily operations of the tribe while maintaining and overseeing economic ventures. The Business Committee is also responsible for overseeing and making decisions relating to sponsorships and assistance sought by various community and civic groups.

The Business Committee is comprised of a chairperson, vice-chair, secretary, treasurer, and three business committee members elected by the General Council for two-year terms. As elected officials, they are responsible for enforcing ordinances, establishing policies, protecting sovereignty and making business decisions in the best interest of the tribe.

The General Council, the legislative branch of the tribal government, is comprised of all tribal members over the age of 21. The General Council is the body where tribal members decide on issues that are relevant to the tribe, develop laws, and make decisions on all major tribal matters.

The San Manuel Band of Mission Indians has also established a strong infrastructure and governmental units designed to manage and govern the tribe and the reservation. The tribe operates and oversees the Department of Health, the Department of Public Safety, San Manuel Fire Department, the Department of Project/Construction Development, and the Gaming Commission.

The San Manuel Band of Mission Indians, an independent and sovereign government, uses revenue generated through different economic development projects to support tribal operations. It provides for the general welfare of the tribe and its members, preserves tribal history and culture, supports economic development to secure the self-sufficiency of the tribe and its members, and provides the infrastructure needed to maintain a viable community on the reservation. The tribal government also assists other tribal nations that do not engage in gaming and generously contributes to local charities.