Souta Tawara had made it clear that he would not inherit his family's udon restaurant when he left his hometown in the Kagawa Prefecture for Tokyo many years ago. But following the death of his estranged father, he finds himself returning to the place he had been so desperate to get away from.

With both parents gone, all Souta expected to find was an empty house and restaurant. Much to his surprise, he stumbles upon a scruffy little boy sleeping inside one of the cooking pots with a sack of flour for a pillow. The boy, as Souta later discovers, is none other than Kagawa's rumored tanuki, a shape-shifting raccoon dog that has been inhabiting the area for many years. Unable to leave the boy to his lonely existence, Souta decides to take care of him and names him Poko.

As Souta spends more time in Kagawa, memories of his childhood resurface, and with them, the regret of having left affairs with his father unresolved. Udon no Kuni no Kiniro Kemari is the story of how, through his innocent ways, Poko unknowingly helps Souta come to terms with his past and their journey toward a new future together.