Nihilumbra is played as a standard platform game, by controlling Born as he walks and jumps across the game's levels. There are multiple enemies that the player needs to avoid since, at first, there is no way to defeat them. The game is divided into the five worlds that Born explores. In each of them, the player is granted a new colour, with which the player can paint on the terrain (by touching the screen) to modify the behaviour of the environment.

Nihilumbra follows the story of Born, who was created from the Void, the nothingness. When he abandons it and appears in the world, he sets up on a long journey where he will learn how to use the colours around him, grating him powerful abilities. The Void from which Born escaped reclaims him, and it will never stop chasing him, devouring everything on its path. As Born runs for his life, he condemns the beautiful places he visits, as the Void makes them vanish forever.