The Japanese releases of the PlayStation 2 and Sega Dreamcast versions of Capcom vs. SNK 2 allowed players on both consoles to play online matches with each other via KDDI Corporation's Multi-Matching service, making it the first video game to allow online cross-play between competing console hardware.

In an 2001 interview featured in the Capcom vs. SNK 2 Another Play Guide, the game's director Hideaki Itsuno stated that there was some demand to include characters like Rain from Plasma Sword, but it was decided against it since they felt characters like that would be too niche and they wanted to prioritize recognition.

In a 2001 interview featured in the Capcom vs. SNK 2 Another Play Guide, it was revealed that the team wanted to include Linn Kurosawa from Alien vs. Predator as a playable character, but that they couldn't do it due to copyright issues. Because of this, they went with Maki from Final Fight 2 instead.

At another point, they considered giving Maki a moveset identical to the one Linn has, but eventually decided against it, instead giving her a moveset that more closely matches the one she had in her debut game.

The game's artist Kinu Nishimura, likely used a picture of Masutatsu Ōyama (more commonly known as Mas Oyama) doing his stance as a reference work for her illustrated work of Ryu.

Eagle's win quotes in the Japanese version of the game are full of sexual undertones, including terminologies 攻め (seme; “attack”) and 受け (uke; “defence”). These terms are used in gay communities in order to describe the active and passive role respectively and are absent in the English release.

In the Japanese version, Rugal Bernstein uses his technique called "Genocide Cutter" and even say it out load, but it was renamed to "Destroyer Cutter" and changed the dub to grunt sounds when he performs his move in the other versions.