Contra 4 is based on the same 2D gameplay system featured in the series up until Contra III: The Alien Wars, ignoring many of the game mechanics introduced in later games such as the fixed weapon configurations in Contra: Shattered Soldier and Neo Contra, returning to the old method of picking up power-up icons to obtain new weapons. The play controls are similar to Contra III, including the ability to hold two weapons in their inventory. The action spans both screens of the Nintendo DS system and a grappling hook can be used by the player's character to latch onto railings, allowing the player's character to move from one screen to the other. Similarly to the arcade version of Super Contra, the player can pick up the same power-up twice, giving them an improved version of the same weapon. The player can also discard a power-up, allowing them to try out a new weapon without losing a previous one, or give the power-up to another player.

In addition to the standard side view stages, there are also tunnel stages similar to the two "3D view" stages from the original Contra, in which the perspective shifts behind the character's back. The action in these stages is displayed solely on the upper screen, while the bottom screen is used to display the stage's map and the locations of power-ups. Other than using both screens, Contra 4 makes no usage of the DS' special features such as touch screen (besides navigating the main menu), microphone, wi-fi support, or single card multiplayer.