Combat in Lion Wars can be compared to board games such as chess, where each piece corresponds to a party member in Ramsar's current warrior list. Each warrior can move around the grid-like board based on his or her movement assignment, or he or she can attack enemy warriors or activate more complex abilities. The terrain of each map determines a fighter's range and mobility. Ramsha's soldiers can be equipped for every job in the Final Fantasy tradition, from standard swordsmen and archers to magic specialists and even more exotic positions such as dragon riders and dancers. Completing actions in battle will gain experience and job points towards each character, the latter of which can be used to purchase new abilities. There are 22 job openings in The War of the Lions. Once a character has learned a skill from a job, they can use it permanently, although only one major set of skills is available at a time and it depends on the job. Many abilities, such as those related to moving or being hit by enemies, can still be equipped if the character later changes jobs. The game also has permadeath - if a character is not healed from excessive damage and incapacitation within a few turns, they are permanently dead and cannot be used again in combat.

Outside of combat, players can walk around the world map. This is unlike other Final Fantasy games where movement is free; instead, Ramza can only move from point to point on the map. Traversing wilderness locations may result in random battles. In towns, players can buy new equipment, recruit new soldiers, and send team members on automated missions to earn cash and other rewards. Later in the game, players can earn additional rewards by poaching creatures during battles.

Another addition to the game is the wireless multiplayer mode, which is available for both cooperative and competitive play. In competitive play, opposing teams may set traps on the battlefield that are hidden from their opponents. For easy identification, teams are assigned colors. The battle ends after a certain number of rounds, and the team with the most HP remaining wins. The winner can then receive randomly generated items from a treasure chest.