In PixelJunk Shooter, up to two players can control their own subterranean vehicles to rescue a number of surviving scientists trapped underground.

In addition to rock and ice, players must manipulate three types of fluid (water, magma, and ferrofluid) in order to reach the survivors.

Originally referred to as PixelJunk 1–4, a 13-day contest was held in which fans submitted game title suggestions to Q-Games.

[6] The game's soundtrack is made up of songs by High Frequency Bandwidth, composed by Alex Paterson and Dom Beken.

[25] The music of High Frequency Bandwidth was also praised, described as "a funky, dynamic collection of upbeat trip-hop" by Eurogamer.

[14] Several reviews made note of said console version's brevity; GameSpot called it "ultimately too short for its own good, abruptly ending just when you're getting into a groove".

Upon entering the Museum, players receive articles of clothing unlocked by completing portions of PixelJunk Shooter.

Q-Games' Dylan Cuthbert said of the title, "it will have some features that are new to the PixelJunk series in general and will be bigger than the first game."