Mitsuha Miyamizu is a high school girl living in the rural town of Itomori near Hida. She is bored living in town and wishes to be a boy in her next life. She inexplicably begins to switch bodies intermittently with Taki Tachibana, a high school boy in Tokyo, when they wake up in the morning. They both initially believe these experiences to be vivid dreams, but eventually realize they can communicate with each other, by recording messages on paper, phones and sometimes on each other's skin. Mitsuha (in Taki's body) sets Taki up on a date with his coworker Miki Okudera, while Taki (in Mitsuha's body) causes Mitsuha to become popular at school. One day, Taki (in Mitsuha's body) accompanies Hitoha and Yotsuha to leave the ritual alcohol kuchikamizake, made by the sisters, as an offering to the Shinto shrine on a mountaintop outside the town. It is believed to represent the body of the village guardian god, ruling over human experiences and connections. Taki reads a note from Mitsuha about the comet Tiamat, expected to pass Earth on the day of the autumn festival. The next day, Taki wakes up in his body and goes on a date with Miki, who tells him she enjoyed the date but also that she can tell that he is preoccupied by thoughts of someone else. Taki attempts to call Mitsuha on the phone, but cannot reach her and the body-switching ends.

Taki, Miki, and their friend Tsukasa travel to Gifu Prefecture by train on a trip to Hida, though Taki does not know the name of the town, instead relying on sketches he has made of the surrounding landscape from his memory. A restaurant owner in Hida, who is originally from Itomori, recognizes one of Taki's sketches. Taki and his friends arrive in the town, which is now destroyed by a meteor and five hundred people were killed, when the comet Tiamat unexpectedly fragmented three years earlier. While seeing the impact crater, in disbelief that everyone he met in Mitsuha's body have died this entire time, Taki sees Mitsuha's messages deleted from his phone and their memories start fading away. Taki finds every names in the record of fatalities and wonders if the body-switching was just a dream. While Miki and Tsukasa return to Tokyo, Taki goes to the shrine alone to drink Mitsuha's sake from the bottle, hoping to reconnect with her body and warn her about the comet. After drinking the sake, Taki lapses into a vision, where he sees Mitsuha's past. When she was a child, Mitsuha's mother Futaba died of an illness and her father Toshiki became the mayor after leaving home, while Mitsuha went to live with Yotsuha and Hitoha. Taki learns that he met Mitsuha on a train three years earlier, when she arrives in Tokyo to find him while the body-switching occurred in her timeline but not yet due to happen for another three years. Before leaving the train in embarrassment, she leaves Taki with the braid, which he wore on his wrist as a good-luck charm.

Taki wakes up in Mitsuha's body at the house on the morning of the festival. Hitoha deduces what happened and tells him the body-switching ability has been passed down among the family caretakers of the shrine. Taki convinces Tessie and Sayaka, two of Mitsuha's friends, to make everyone evacuate the town, by disabling the electrical substation and broadcasting a false emergency alert. Realizing that Mitsuha is in his body at the shrine, Taki returns to find her and Mitsuha wakes up in Taki's body. When Taki reaches there during the sunset, the two sense each other's presence, but are separated temporally by three years and cannot see each other. When twilight falls (referred to in the film as "magic hour" or "kataware-doki"), they return to their own bodies and see each other in person. As Taki returns the braid to Mitsuha, they attempt to write their names on each hands so they will remember each other, but twilight passes and Mitsuha disappears before she can write hers. When the evacuation plan fails, Mitsuha determines to convince Toshiki and evacuate the town. Before doing so, Mitsuha notices her memories of Taki are fading away, and discovers he wrote "I love you" on her hand instead of his name. Despite the evacuation, the meteor crashes to Earth and still destroys Itomori. Taki wakes up in his own time, remembering nothing.

Five years later, Taki has graduated from university and searches for a job. He senses he lost something important he cannot identify, but feels drawn to the town's disaster, in which the inhabitants had survived under Toshiki's order. One day, Taki and Mitsuha see each other when their trains draw parallel, and they separately disembark and search for each other, finally meeting at the stairs of Suga Shrine. Taki calls out to Mitsuha, saying that he feels that he knows her, and she responds that she has the same feeling. With their connection re-established, they shed tears and simultaneously ask for their names.