Frustrated with her mundane high school life in the town of Itomori, Mitsuha Miyamizu has longed to live as a boy in the Tokyo metropolis. One day, the fantasy she has always dreamed of comes true—awakening in a boy's body and experiencing the thrills of the city. Meanwhile, high school student Taki Tachibana finds himself waking up as a girl living in a lakeside town by the mountains, the complete opposite of the Tokyo life that he is familiar with.

As Mitsuha and Taki discover they are living the lives of one another in their dreams, the two begin working together to adjust to this new reality. Little do they know, their fragile relationship soon prompts the pair to search for each other in fierce defiance of the thin thread of fate that connects them.