A flagship is a vessel used by the commanding officer of a group of naval ships, characteristically a flag officer entitled by custom to fly a distinguishing flag. Used more loosely, it is the lead ship in a fleet of vessels, typically the first, largest, fastest, most heavily armed, or best known.

Over the years, the term "flagship" has become a metaphor used in industries such as broadcasting, automobiles, education, technology, airlines, and retail to refer to their highest quality, best known, or most expensive products and locations.

In common naval use, the term flagship is fundamentally a temporary designation; the flagship is wherever the admiral's flag is being flown. However, admirals have always needed additional facilities, including a meeting room large enough to hold all the captains of the fleet and a place for the admiral's staff to make plans and draw up orders. Historically, only larger ships could accommodate such requirements.

The term was also used by commercial fleets, when the distinction between a nation's navy and merchant fleet was not clear.

In the age of sailing ships, the flagship was typically a first rate; the aft of one of the three decks would become the admiral's quarters and staff offices. This can be seen on HMS Victory, the flagship of Admiral Horatio Nelson at the Battle of Trafalgar in 1805, still serving the Royal Navy as the ceremonial flagship of the First Sea Lord from Portsmouth, England.

In the 20th century, ships became large enough that the larger types, cruisers and up, could accommodate a commander and staff. Some larger ships may have a separate flag bridge for use by the admiral and his staff while the captain commands from the main navigation bridge. Because its primary function is to coordinate a fleet, a flagship is not necessarily more heavily armed or armored than other ships.

Modern flagships are designed primarily for command and control rather than for fighting, and are also known as command ships.

As with many other naval terms, flagship has crossed over into general usage, where it means the most important or leading member of a group, as in the flagship station of a broadcast network. The word can be used as a noun or an adjective describing the most prominent or highly touted product, brand, location, or service offered by a company. Derivations include the "flagship brand" or "flagship product" of a manufacturing company, "flagship store" of a retail chain, or "flagship service" of a hospitality or transportation concern.