Delivery God Yato, a deity of little repute and without worshippers, seeks odd jobs for five yen in order to create wealth that could enable him to acquire a shrine. A significant challenge he faces is the lack of a "Shinki"; his weapon partner has resigned, feeling disenchanted with a god without a home. Consequently, Yato tries to find a new companion while taking on more jobs.
On one of his tasks, Yato encounters a missing cat and gives chase, leading him into a collision with a car. Hiyori Iki, a nearby girl, rushes to save him but ends up getting hurt instead. In the hospital, she realizes that the crash has separated her soul from her body, which motivates Yato to help her, for a fee of five yen. However, Yato requires a new Shinki to achieve this, and he finds one in the rebellious spirit named Yukine.
Noragami narrates the story of a girl navigating between two worlds and a wandering deity's pursuit of a place to call home.