A Commander-in-Chief (abbreviated CinC or CINC) is the supreme commander of an entire military force or at least a significant portion of the total force. The role is usually filled by an officer with the highest rank possible in the organization.
Starfleet's Commander-in-Chief was a position held by the senior fleet admiral, who took orders only from the Federation Council and its President. The post was also referred to as Commanding Admiral (Star Trek: The Motion Picture novelization) and Commander, Starfleet. (Star Trek VI: The Undiscovered Country, Star Trek III: The Search for Spock)
From 2270 to the mid-2280s, the position was held by Fleet Admiral Heihachiro Nogura. He retired around 2285 and was replaced by Harry Morrow. (TOS novel: The Lost Years; Star Trek: The Motion Picture, Star Trek III: The Search for Spock, Star Trek: Pendragon)
In 2293, Fleet Admiral William Smillie was the C-in-C. Though he was not involved in Admiral Cartwright's conspiracy, he nonetheless resigned in shame after the Khitomer Conference, and was succeeded by Androvar Drake. Unfortunately, Drake himself had been a member of the conspiracy, and his actions as C-in-C nearly led to a war between the Klingons, Romulans and the Federation before his death at Chal. (TOS novels: Star Trek IV: The Voyage Home; The Ashes of Eden; Star Trek: Pendragon)
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William Smillie resigned from the post in December 2294, after the apparent death of James T. Kirk and the suicide of John Harriman. Lystra Davis, a former commanding officer of the Yorktown, succeeded Smillie. (Orion Press: Chekov's Enterprise)
In Star Trek: Pendragon, after the previous C-in-C resigned in 2372, Chief of Starfleet Operations Vice admiral James Leyton was appointed acting Commander-in-Chief, giving him the opportunity to stage his military coup. (DS9: "Homefront"; PDN: "Sword of Damocles")
In Star Trek: Pioneer, the position of Commander-in-Chief of Starfleet is referred to as the Starfleet Commander. The Starfleet Commander acts in much the same way as the Chairman of the Joint Chiefs of Staff in the United States government of the 20th century. The Admiral holding the position of Chief of Starfleet Operations is the second-in-command of Starfleet. When the Starfleet Commander retires, leaves office, or dies in office, a special committee made up of high ranking Starfleet captains is convened to select a replacement. The Federation President can make a recommendation. In the result of a tie between the candidates for the position, the President's recommendation is selected.
In 2380, Admiral Harold Anton became the Starfleet Commander after the death of Admiral John Hayes. Captain Benjamin Kelsoe, along with Captain Sarah Tellening, Jean-Luc Picard, and other prominent Starfleet captains choose Anton over Admiral Dustin McCloud. ("The Teacher")
When the Federation established a full Federation military, the two new branches of the Federation military were given positions equivalent to the Commander-in-Chief: the Commandant of the Marine Corps and Chief of Staff of the Starfighter Corps. In 2383, the C-in-C was Thomas Crowe.
In the Starfleet Command (RPG) continuity, Fleet Admiral Hunter Dunbar took over as the Commander-in-Chief in 2385 after James Anders was elected as the President of the United Federation of Planets. Dunbar was hand-picked by President Anders after he received news of the election.
Admiral Conrad Slater is forced to step down in 2243 after two years of near constant defeat at the hands of the Klingon Empire following the start of the Four Years War. He is replaced by Admiral Marcus Ramirez. One of Ramirez' first acts is to order the design and construction of what would be known as the Ares-class Battle cruiser.