Starfleet Command's logo
Starfleet Command was the operating authority of Starfleet and, before that, Earth Starfleet. Its headquarters were located in San Francisco on Earth. Starfleet Academy was also located in the same area in San Francisco.
There was at least one additional office of Starfleet Command which was located in Chicago. Commander-in-Chief Thomas Crowe was known to prefer his office in Chicago, as he liked the cold weather. (Star Trek: Remington)
External links
Starfleet Command article at Memory Alpha, the canon Star Trek wiki.