The central concept of Fossil Fighters is the revival of prehistoric fossils into supernatural forms known as "vivosaurs", charged with elemental energy, and the use of these creatures in combat against each other.
The player accesses regions called "dig sites" and collects "Fossil Rocks", each of which contains one-quarter of a dinosaur's skeleton; head, body, arms, or legs. Fossil Rocks are scanned and cleaned at a "Revival Machine" and then incorporated into a vivosaur. Although a vivosaur can be revived using only a head fossil, integrating the other three parts will grant it bonus strength and access to additional abilities. If the secondary parts are found without a head, they will be stored until the head is found and subsequently integrated into the vivosaur.
Cleaning a Fossil Rock involves removing the rock around the fossil with a hammer, and then the remaining layer of dirt with a drill. The player has 90 seconds to accomplish this task and risks damaging the fossil by hitting it directly with the hammer or drill. A cleaner and less damaged fossil grants more strength to the vivosaur it is integrated into.
Vivosaurs with a head fossil integrated are used in turn-based combat against opposing vivosaurs. Up to three of the player's vivosaurs may challenge up to three of an opponent's. Each team has access to one Attack Zone, two Support Zones and one Escape Zone; their starting positions are in the Attack and Support Zones. Vivosaurs can use attacks and other abilities by expending Fossil Power (FP) gained at the start of each turn. Fossil Power can also be conserved between turns in an attempt to expend a large amount on a strong attack. Two turns’ worth of Fossil Power is added to a combatant's pool if one of their vivosaurs runs out of Life Points (LP) and is defeated. LP also decides who is first to attack in a battle, in which the team with the lowest total LP goes first. The battle is over when all of an opponent's vivosaurs are defeated.
The basic strategy of Fossil Fighters is to use attacks with an Attack Zone vivosaur while Support Zone vivosaurs apply statistical bonuses to the player's Attack Zone or statistical penalties to the enemy's Attack Zone. However, Fossil Fighters contains much strategic diversity. A damaged Attack Zone vivosaur may be "escaped" to the Escape Zone when weakened, but a Support Zone vivosaur must enter the Attack Zone and take its place. The now-empty Support Zone will be filled by the escaped vivosaur in two turns.
Fossil Fighters uses a system of elemental balance where each vivosaur has an elemental affinity: Fire is weak to Water, Water is weak to Air, Air is weak to Earth, Earth is weak to Fire, and Neutral-element vivosaurs have no elemental strength or weakness. Certain mythical vivosaurs, only granted to the player in special circumstances, are of the "Legendary" element, which functions identically to Neutral-element vivosaurs.