PixelJunk Shooter Ultimate combines the individual titles PixelJunk Shooter and PixelJunk Shooter 2 into a single, seamless game. For PC only the first game was previously available and player can continue their progress in Ultimate after finishing the first PixelJunk Shooter. For both PS4 and PS Vita this is the first release of the game for the platform.

The graphics have been reworked into a higher definition, the HUD has been redesigned and the player's main space ship has a new look. The visual effects of the substances and lightning also received a distinct makeover. It retains the multiplayer options of the original titles. The single-player campaign can be played cooperatively locally / offline with another player, while online multiplayer introduced in the second game has one-on-one fights in a global league battle.