Starfleet Command is the operating authority of Starfleet, the exploratory, scientific, and military department of the United Federation of Planets. The organization's primary management center is located at Starfleet Headquarters in San Francisco. Starfleet Command is responsible for overseeing the operational duties of it's fleet as well as overseeing the various other branches of Starfleet. In essence it is the central authority of Starfleet and where all centralized orders come from. Because of the time delays involved in many subspace communications, Starfleet Command also includes a network of administrative and support outposts known as starbases throughout the Federation. Starfleet's starships operate out of these starbases under the supervision of various admirals, the senior officers of the fleet.

Starfleet Command operates ten fleets and thousands of starships. Each fleet commander reports directly to the Chief of Starfleet Operations who has direct control over the day to day operations of the fleets various starships, starbases and outposts. The CSO then is under the direct supervision of the Chief of Staff of Starfleet who has less direct, but more broad operational oversight of the fleet, who in turn reports directly to the Commander in Chief of Starfleet who is the Federation President's direct military advisor.

The Commander in Chief is a position normally assigned to a Fleet Admiral. The Chief of Starfleet Operations and Chief of Staff of Starfleet typically hold the rank of Admiral or Fleet Admiral. The ten fleet commanders are typically positions held by Admirals or Vice Admirals who are given relative freedom in choosing their fleet staff. Each different administrative branch of Starfleet Command outside of the main fleet vary in their size, positions available and ranks of their commanding officers.