The Sheriff is elected to a four-year term and appoints an Undersheriff who serves as his second in command. Sheriff Mark McCloskey is the Chief Executive Officer (CEO) of the agency and the Undersheriff is charged with insuring the operational and administrative functions of the Sheriff's Office are performed in a professional manner.

The Administrative Captain serves as the agency's Accreditation Manager and also oversees the Professional Standards function. The Administrative Lieutenant oversees the hiring of new deputies and the training function as well as coordinates security measures at McGee Park, the San Juan County Fairgrounds. The Training Coordinator is responsible for the hiring process for new deputies and training both new hires and incumbents. He also instructs at the Basic Academy and in-service training events.