Mega Man Battle Network is a real-time tactical RPG series. To progress through the games, the player must alternately navigate the outside world as Lan Hikari and the Net as MegaMan.EXE, each containing certain tasks that must be completed to allow advancement in the other. Controlling Lan, the player may travel around the world map, interact with non-player characters, check email, purchase items, initiate Net missions, or speak with MegaMan.EXE through his PET. In contrast with traditional Mega Man entries in which battle and movement through the levels happen in the same setting, Battle Network's combat occurs only through by battling computer viruses within the Net. This cyber world is represented by a series of branching pathways and nodes, where MegaMan.EXE can travel to both new and previously visited locations, find and purchase items, and fight viruses. Battles do not generally appear on the field screen of the Net but are usually set as random encounters.

The battlefield itself is made up of 18 tiles divided into two groups of nine, one group being space in which MegaMan.EXE may freely move and the other group being space inhabited by enemies. Akin to other Mega Man games, MegaMan.EXE possesses an arm cannon called the "Mega Buster". The player can transition among the nine provided tiles and fire the Mega Buster at enemies from across the screen. The objective of each battle is to delete all the viruses by reducing their hit points (HP) to zero. If MegaMan.EXE's own health depletes, a game over occurs. In order to attack without the Mega Buster, the player must utilize Battle Chips, which are placed into a "folder" before the battle starts, and are drawn at random. Starting with the third game, Battle Chips are organized into three primary categories which limits how many of the same chip can be used in the same folder: Standard (4 of the same, 30 in the folder), Mega (1 of the same, 5 in the folder), and Giga (only 1 per folder). Excluding the asterisk code, which was introduced in 2, the player can only use Battle Chips that have either the same, or share the letter. Selecting a specific combination of Battle Chips results in Program Advances, which give the player either a strong attack, or continual use of the Battle Chip used for several seconds. Each Battle Chip also has an element assigned to it, and hitting an enemy with its weakness will result in them taking double damage.

The series also has multiplayer functionality where two players can either fight, or trade chips with each other using the Game Link Cable; trading the opposite version's Mega Chips in 4–6 will result in them appearing as "Secret Chips" in the Chip Library, however Giga Chips cannot be traded .