Ys Origin is an action RPG set 700 years before Ys I & II, detailing the demons' assault on the land of Ys and the subsequent disappearance of its ruling Goddesses. Players control one of three distinct characters, each offering a unique narrative perspective on the events unfolding within the Devil's Tower. The game refines the action-RPG formula established in previous entries, blending arcade-style platforming and Metroidvania exploration with a multi-layered story.

The game's progression involves navigating the Devil's Tower, overcoming screen-filling bosses with complex AI, solving environmental puzzles, and engaging in platforming challenges. Ys Origin provides five difficulty settings, from Very Easy to Nightmare, catering to a range of player skill. Additional replayability is encouraged through unlockable modes such as Time Attack, Boss Rush, and Arena Mode, which challenges players with large enemy waves. The title supports high-resolution graphics with widescreen capabilities and fully configurable controls.