A chronometer is a device used to keep track of time. Starships measure the passage of time when they traverse the space-time continuum other than Albert Einstein's proper time by use of chronometers. (TOS: "The Naked Time", "Tomorrow is Yesterday", "The Mark of Gideon")
On occasion, starships may need to reset the on-board chronometer, at which time a Federation time beacon may be consulted. (TNG: "Cause and Effect")
In "The Naked Time", the original version featured a mechanical chronometer. In the remastered version, it was changed to a digital display.