The guidance system was a set of devices that was used to navigate a starship or other self-propelled device.

Doctor Timicin of Kaelon II modified the guidance system of Starfleet photon torpedoes. Those modified torpedoes would enable him to implement his theory of helium fusion enhancement and possibly revitalize the Kaelon sun. (TNG: "Half a Life")

In early 2373, Captain Benjamin Sisko theorized that a possible reason for the Vorta commander Kilana's interest in a downed Jem'Hadar attack ship was that she wanted to recover its guidance system. (DS9: "The Ship")

The guidance system of the same Dominion ship, used by Captain Sisko and his crew to destroy a Dominion ketracel-white facility in 2374, was damaged during the facility's destruction. (DS9: "A Time to Stand")