The game saw a simultaneous August 8, 2003 release in Japan on the WonderSwan Color and Swan Crystal titled Rockman EXE N1 Battle.

In this game, the player duels a single opponent simply by setting up 12 Battle Chips on a grid called a "Program Deck".

[6] The game selects three chips at random on one of the grid's rows, and the player's Navi uses them consecutively, ending the turn with that character's signature attack.

If ten turns pass and neither competitor has lost all of their HP, the game determines the winner based on how many chips are left in their decks.

Winning every fifth battle in one of these earns the player a new Navi Chip to use as well as a variable amount of "Zenny", the game's currency.

[9] The game contains six different playable pairs of operators and their NetNavis including Lan and MegaMan, Dex and GutsMan, Mayl and Roll, and Chaud and ProtoMan.

[12] Mega Man Battle Chip Challenge was not well received by most reviewers, currently holding an average score of 49,90% on GameRankings and a 54 out of 100 on Metacritic.

[6][8] The GBA version of Mega Man Battle Chip Challenge was the 22nd best-selling game in Japan during its release week at 7,403 copies sold.