In the Mega Man Zero 2, the gameplay remains almost identical to the first game with some new additions. The player still navigates Zero through obstacles and terrain while fighting enemies. In this game however, Zero can now learn EX Skills, similar to past techniques from the Mega Man X series for his Z-Saber, such as the Tenshouzan attack and a few new attacks as well. New to the series is the Form System, which changes the way Zero fights, based on the color scheme he changes into. There are up to a total of nine forms to unlock which can be obtained under circumstances such as destroying enemies with a certain weapon.

The Cyber-elf system and Rank system return, but the player is required to be less reliant on the Cyber-elves if a higher rank is desired. Weapons returning from the first game are the Z-Saber, Buster Shot and Shield Boomerang. The Triple Rod has been replaced by the Chain Rod, a hookshot-like weapon created from fragments of the destroyed Triple Rod. The Chain Rod can be used to pull in enemies, objects and items alike as well as swing whilst attached to a ceiling.

Unlike the previous game, the player cannot evacuate and skip active missions, but instead can escape revisited stages after completed missions, in similar way to Mega Man X series.

Just like in the first game, a "New Game Plus" can be played by clearing the game and loading the completed save file. In the new game, Zero will start with all activated Cyber-elves used from the previous game still in effect (the penalties, however, will still remain). Zero will also retain any EX Skills and alternate forms that he earned in the previous game as well.