The game's story centers around a war between the kingdom of Ragnanival, led by the king Odin, and the realm of Ringford, led by the queen Elfaria. Their war has devastated the country of Valentine, of which only scattered ruins remain. The story is told from the perspective of five characters whose stories intertwine: Gwendolyn, valkyrie and younger daughter of Odin; Cornelius, prince of the neutral country of Titania; Mercedes, daughter of Elfaria and princess of Ringford; Oswald, a shadow knight and agent of Ringford; and Velvet, a survivor of Valentine's devastation.

Odin Sphere Leifdrasir: Chiisana Yousei Joou is based on Vanillaware's 2D action RPG Odin Sphere Leifdrasir.