Subaru Mikazuki is a 23-year-old mystery novel author, major introvert, and an awkwardly shy person. He would much rather stay home to read a book than go outside and interact with others. Further exacerbating this life of solitude, his parents tragically died in an accident many years ago, leaving him alone in the world.

One day, while giving offerings at his parents' grave, Subaru runs into a small grey and white cat named Haru, which he ends up taking home with him. Subaru, however, has never taken care of anyone else in his life—can he even take care of a cat? Haru is grateful toward Subaru, as he gives her all the food she wants—a luxury for a cat who is used to a rough life on the streets. But she notices that Subaru can't even seem to take care of himself! Will she be okay with this dunce?

Doukyonin wa Hiza, Tokidoki, Atama no Ue. tells the story of an unlikely friendship between a human and a cat who try to foster an understanding with each other.