Gameplay in Final Fantasy XI Online consists of two major components: quests, which do not advance the main storyline but fill out the fantasy world of FFXI, and missions, through which the main storyline of the game is told.

Quests may be undertaken for various rewards, including money, items which cannot be acquired any other way, or simply prestige. Final Fantasy XI's quest system includes a mechanic whereby fame is accrued through the completion of quests. Each city and major area has its own fame rating, and more quests open to players as they grow in fame in each area. While quests do not directly advance the main stories of FFXI, they may fill in some additional details that would otherwise be missed.

Missions are undertaken to advance in rank, to access new areas and gain new privileges, and to advance the various plotlines in the game. Each country has its own set of missions, which a player must complete to advance in rank; a player may only complete missions for his home country, resulting in some players completing all of a country's range of missions, only to switch allegiances to see another country's storyline. The newest storylines are often not available in their entirety at first, and are unlocked gradually over time. In addition to completing quests and missions, players can participate in several side activities : harvesting, excavating, logging, mining and fishing.

Although there was not an initial system allowing players to compete in battle with each other, it was eventually added to the game. Final Fantasy XI Online 's Player vs. Player (PvP) system is unique among MMORPGs in that players may only compete directly against one another under very specific circumstances. PvP happens only in "matches" that players enter by their own consent; players cannot attack one another outside of these circumstances. Players who are defeated in a PvP match do not lose experience points, and they cannot lose items or equipment from being defeated.

One of Final Fantasy XI Online's most dynamic features is the flexibility of its job system, adapted from previous Final Fantasy titles. Players are able to change their jobs any time they wish and eventually gain a "support job," allowing the player to learn additional skills and try different combinations. Each job has unique abilities, which must be activated by the player in order to come into effect, last a limited time, and have a "cooldown" period before they can be used again; traits, which are passive abilities that are always in effect; and a special "2-hour" ability that performs some extraordinary function and has an extraordinary 2-hour-long cooldown period to go with it.

Battles in FFXI take place in the same world in which players move around, unlike previous FF games in which a battle would take place in a new screen. Players may be attacked by aggressive creatures, or they may attack creatures themselves.

Monsters in FFXI operate under a complicated system of "claim" and "hate". A monster is "claimed" the moment a player performs any action upon it, whether attacking it or casting a spell. Once it is claimed, it can only be attacked by players in the party or alliance of the player that claimed it. Unclaimed, a monster's name is yellow; a claimed monster's name will appear red to players in the immediate party of the claimer, and purple to anyone else, including anyone in the player's alliance. If players find themselves unable to handle a monster they have engaged, they can "call for help." The monster's name turns orange, players in the immediate vicinity are alerted to the danger, and anyone can attack the monster. However, no experience or items result from the monster's death in this situation.

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