Zone of the Enders: The 2nd Runner - Special Edition was released in both Europe and Japan after the North American release of the vanilla version. This version of the game includes several minor game improvements and few extras :

- New difficulties Super Hard (Japan version) and Extreme
- Graphical and framerate enhancements
- A couple of new 3DCG cutscenes
- New battle sequences at certain parts of the game
- New extras missions
- Mechs in VS. mode consume subenergy when using special attacks
- Added subweapon practice simulations and explanations in VR Training mode