Age of Mythology is a real-time strategy game and a spin-off of the Age of Empires series, which retains many gameplay elements from the previous installments. Instead of multiple civilizations, as in Age of Empires, it offers three unique factions: Greeks, Egyptians, and Nordics. Each of these factions differs not only visually, but also functionally - they have a different economic model, technology tree, set of units, and play style. A key element is also gaining favor from the gods, which is different for each faction.

Age of Mythology introduces a 3D engine and mythological units and heroes. Players can choose gods to worship, who are divided into major and minor. Major gods act as sub-factions, offering unique bonuses and abilities. As players advance to subsequent eras, players can choose minor gods, who introduce unique units, upgrades, and abilities. Mythological units can be trained in temples, and their production requires gaining favor. Heroes are particularly effective against mythological units, and some units have special abilities, such as Anubites' jumps or Minotaurs' throwing of enemies.

Changes to the game's economy include unlimited food sources, such as farms and schools of fish. Age of Mythology's campaign, titled "Fall of the Trident", consists of 32 missions. The story combines the stories of all three factions, whose heroes - the Greek Arkantos, the Egyptian Pharaoh Amanra, the Greek heroes Ajax and Chiron, and others - work together to stop pirates and followers of the evil cyclops Garganensis from freeing the imprisoned Titan. Skirmishes and multiplayer matches take place on randomly generated maps with different templates and game modes.