Sky Runner Deep Space is a classically designed platformer that puts players in the role of an agile alien. Set in a dangerous galactic environment, the character must navigate through various sectors ranging from abandoned moon stations to the edges of a black hole. The core objective of the game is to collect all hidden energy crystals in each of the seven levels. Only once the collection is complete does an exit portal stabilize, allowing passage to the next sector. In addition to collecting crystals, the focus is on a race against time, as the system precisely measures the duration and records best performances in a high-score list.

The controls are based on the arrow keys or the WASD layout for movement and jumping. A special feature of the gameplay mechanics is the rocket mode, which is activated via the Z key. This boost allows the player to cover additional distances or reach heights that would be inaccessible with a simple or double jump. Since rocket fuel is limited, tactical use of this resource is crucial for success. Visually, the title utilizes the Pyxel engine for a minimalist 16-color retro aesthetic. Obstacles such as moving platforms and dangerous space spikes demand high precision from the player as they work their way through areas like the asteroid belt or the nebula passage toward the galactic center.