Ballpoint Universe is a side-scrolling shoot 'em up entirely drawn as doodles with a ballpoint pen. The different levels are accessed through a large hub played as a platform game. Called Entrino City, it is a safe environment where the main character can be guided around and jump to explore the surroundings. Passages are used to move forwards or backwards across the planes and there are very minor puzzle elements where raising a platform for instance opens up a new path. Entrino City has a conflict with creatures known as Logicians who have taken over the surroundings. The citizens have resorted to building fighter ships with the parts that were left behind. In the hub there are different characters to talk to, often to access missions, hidden golden sketches to collect and a casino game where prizes can be won.
Once a shoot 'em up mission is accessed, the character first needs to outfit his ship based on four elements: primary weapon, secondary weapon, nose and wing. For each type there are multiple configurations that are unlocked with ink, the game's main currency. There are melee weapons that do a lot of damage up close, and also long-ranged weapons to shoot far across the screen. Other options include super weapons, shields, additional health and a module that attracts all nearby ink to absorb it. Each element can be upgraded two times.
Ink is collected by completing missions and left behind by defeated opponents. The ship has a number of lives and can take a limited number of hits before it explodes and a life is lost. The collected ink also builds up a meter. Once a full star is visible, a special option can be activated, such as a powerful weapon or a shield. It is possible to build up multiple stars, but a single hit removes all of them right away. Each mission has a different environment and new types of enemies. After each mission the player receives a bronze, silver or gold medal based on performance. From the main hub it is possible to replay any mission right away.
Originally released as Ballpoint Universe, it received the Infinity subtitle after the addition of an infinity game mode with an endless amount of waves.