Fleet captain was a Starfleet title given to a senior captain with a different set of responsibilities than a starship captain. This may have been a higher rank than captain or even commodore, although it did not possess a permanent position in the rank hierarchy.

In 2264, after promotion to fleet captain, Christopher Pike passed command of the starship USS Enterprise on to Captain James Kirk. In 2266, as a fleet captain, Pike was engaged in a training exercise aboard an antiquated Class J starship. The vessel's baffle plate ruptured and many of the trainees were killed. A number were saved by Pike--at the cost him being rendered a "complete invalid". Despite his catastrophic injuries, Pike remained on the active duty roster as a command-grade officer. (TOS: "The Menagerie, Part I", "The Menagerie, Part II")

In the 2260s, Fleet Captain Garth was one of Starfleet's most decorated captains, the hero of the Battle of Axanar. Garth was injured and recovered among the natives of Antos IV, where he learned of the Antosians' bizarre metamorphic biochemistry control. The strain on Garth's system was too much, he was driven insane by learning their abilities. His life was saved, but maddened, he ordered a starship to fire on the planet, the crew mutinied and Fleet Captain Garth was sentenced to treatment at Elba II. (TOS: "Whom Gods Destroy")