The game followed the typical eight-way directional pad/stick with six-button layout common to most fighting games at the time (more commonly in this case, Street Fighter II). Since the standard Mega Drive/Genesis controller has only three action buttons, players would have to purchase a six-button controller or Sega Activator, or else use the start button to toggle the action buttons between punches and kicks. The joystick or D-pad is used to move away, towards, jump and crouch. There are three punches and three kicks that vary based upon speed and power. The weakest punches and kicks are fast but do minimal damage, medium attacks are a balanced mix of recovery speed and damage, and strong attacks are the most powerful but recover the slowest. Attacks can be blocked by pressing away (for high attacks) or down and away (for low attacks). Grapples are executed by standing close to an opponent and pressing toward or away and using either the medium or the strong punch button. These attacks cannot be blocked or escaped.
Each character has their own unique special attacks that are performed differently from those of other characters. If a character is hit several times in a row they become "dizzy" and their opponent can land a free attack. In Eternal Champions, all special move commands are performed by either pressing multiple buttons together, or holding back or down to charge and then pressing towards or up together with a button. There are no rolling motions in this game, and a given special move may only be performed with a specific button.