Both editions of the game feature slightly different jack in animations in Japan. The animation was removed from the international release of the games, instead featuring a short white flash.

Meant to be a revised version for bug fixes and whatnot, Rockman.EXE3 Black was released in Japan some time after the initial EXE3 was released. Black was released internationally as Battle Network 3 Blue and regular, no-color EXE3 is known as Battle Network 3 White internationally. There are many differences between the two, such as an exclusive battle against Punk in Blue/Black, different color schemes for buildings and objects (the squirrel is ACDC park is an example), different Giga Chips, and Style Changes exclusive to each version.

There are actually four versions of Mega Man Battle Network 3. Rockman EXE 3 (with no color version) and Rockman EXE 3 Black Version were only released in Japan. Outside of Japan, the game was released in two different versions: White and Blue, which were seemingly based on Rockman EXE 3 and Rockman EXE 3 Black, respectively. This also marks the beginning of Capcom's trend of releasing two versions of every main series game.

Lan's grandfather Tadashi Hikari greatly resembles Dr. Light, known in Japan as Dr. Right, from the original Mega Man series.

The chinese characters in Tadashi Hikari's name reference both of these spellings, with 光 (Hikari) meaning "Light", and 正 (Tadashi) meaning "Right", as in "correct" or "just".