Fleet captain

Fleet Captain is a Starfleet title given to a senior captain with a different set of responsibilities than a starship captain. This could be thought of as a higher rank than captain, although it does not possess a permanent position in the rank hierarchy (a captain could also be directly promoted to commodore, the next highest rank, without spending time at a fleet captain posting).

Fleet Captain is a rare military title that may be bestowed upon senior naval captains for a variety of reasons, the most common of which is to temporarly take command of more than one vessel. The rank can, therefore, be interpreted as a close equivalent to Commodore or to the 19th century rank of Flag Officer. The main distinction of a Fleet Captain is that normally the title is strictly temporary for the duration of a single mission.

From Memory Alpha -- the free Star Trek reference