Neo Contra once again brings the games arena back into three dimensions. However, unlike the titles developed under Appaloosa Interactive, players only need to aim in third dimension upon rare occasions. Additionally, this title eradicates the boss-oriented gameplay of Hard Corps and the previous 32-bit titles, and seeks a balance more reminiscent of the 8-bit and SNES Contra games; long free-form shooting sections, interspliced with boss encounters.
Additionally, gameplay varies depending upon the level and camera angle presented (the camera cannot be user-controlled). Most of the game is played in an isometric perspective, but portions are side-scrolling or overhead-behind. The player cannot jump. Instead, two new defensive moves are added that allows the player to effectively evade in the new dimensions: dash and spin. Dash gives the player a quick burst of speed to evade hostiles, while spin gives the player an instant of invulnerability. The hit-ratio system that was introduced in Shattered Soldier has been kept in this title.
The game uses a modified version of the three-weapon configuration from Shattered Soldier. The player has two types of firearms used against ground-level targets, one with regular ammo and the other with flammable rounds, and a third weapon used to lock-on airborne targets. The player can choose from one of the three initially available weapon sets (one which includes the famous Spread Shot from the earlier Contra games, which was missing in Shattered Soldier), with three additional sets that are time-release. The Type F configuration features the GV Laser and Ripple Laser, both weapons from Gradius V.