Main menu screen.

The gameplay of Final Fantasy III combines elements of the first two Final Fantasy games with new features. The turn-based combat system remains in place from the first two games, but hit points are now shown on top of the target when attacked or healed, rather than captioned as in the original versions of the previous two games. Auto-targeting for physical attacks after a friendly or enemy unit is killed is also featured for the first time.

The experience point system featured in Final Fantasy makes a return following its absence from Final Fantasy II. A class system is also featured; however, unlike in Final Fantasy I, where the player chooses each character's class alignment at the start of the game, and Final Fantasy II, where there are no specific classes, Final Fantasy III introduces the "job system" for which the series would become famous. Jobs themselves are basically interchangeable classes: In the original version of the game, all four characters start out as "Onion Knights," but before long the player is given the option to have them switch to a variety of other classes. Final Fantasy III is the first game in the series to feature special battle commands such as "Steal" or "Jump," each of which is associated with a particular job ("Steal" being the Thief's speciality, while "Jump" is the Dragoon's forte). It is also the first game in the series to feature summoned creatures and their "Summon" skill.

Several classes were altered (such as additional abilities) in the Nintendo DS version to improve balance.