Following the lead of Nintendo's earlier Mystery Dungeon games, Explorers of Time transports DS gamers to a land before humans where, instead of playing as a trainer, they take the first-hand role of a pocket monster. In the beginning of the game, players answer a series of questions to help them decide which Pokémon to play as. The role-playing adventure involves befriending other Pokémon and exploring randomly generated dungeons where enemies and treasure await.

As is tradition for Pokémon handheld games, Pokémon Mystery Dungeon: Explorers of Time is released alongside a companion game, Pokémon Mystery Dungeon: Explorers of Darkness, which features the same basic story and gameplay with slightly different character choices and quests. Two DS Mystery Dungeon Explorers players can team up through a wireless connection, to trade, text chat. And complete rescue missions together.