Miitopia plays like a classic JRPG, with the main feature in this game being the use of Miis as characters populating the world, allowing you to choose from your own Miis for the roles of your playable characters and major NPCs, while allowing the use of Spotpass for casting minor NPC roles. Besides being able to directly choose which Mii gets each role, the game can also do that automatically.

A simple job system is in place, giving you the ability to choose a job for each character that joins the party, each with their particular strengths and weaknesses. There are the usual jobs in the genre, like warriors, clerics, mages, besides more unusual ones, like cats. Equipment is progressively stronger, making it easier to improve growth, and food items can also be used to boost character stats. The battle system follows the traditional turn-based formula, with only the main character being controlled directly, even though there is an option for auto-battle, as well as fast-forwarding.

One aspect that is different from usual is the use of relationships between characters as a game mechanic, in that having a good relationship between two characters will have them help each other out in battle (for instance, through the use of healing items).

Miis can be transferred from the Tomodachi Life game, or from the Miitomo smart-device app. The game also supports Amiibo functionality, which provide customization to the Miis.