Makoto Konno (Riisa Naka/Emily Hirst), a girl attending high school in Tokyo's shitamachi, realizes she has the power to go back in time and re-do things (called a "time-leap") when she impossibly avoids a fatal accident at a train crossing one day.
Bewildered, she consults with her aunt (Sachie Hara/Saffron Henderson) throughout the film, who is implied to be Kazuko Yoshiyama, the protagonist of the original novel. At first, Makoto uses her power extravagantly to avoid being tardy and to get perfect grades on tests, and even relive a single karaoke session for about ten hours. However, things begin to turn bad as she discovers how her actions can adversely affect others.
Makoto ends up using up more of her leaps to recklessly prevent undesirable situations from happening, including an awkward confession of love from her best friend Chiaki Mamiya (Takuya Ishida/Andrew Francis). Eventually she discovers a numbered tattoo on her arm which counts down with each leap. She determines that the tattoo indicates that she can only leap through time a limited number of times. With only a few time leaps left, she attempts to make things right for everyone, but impulsively uses her final leap to prevent a phone call from Chiaki asking if she knows about time-leaping. As a result, she is unable to prevent her friend Kōsuke Tsuda (Mitsutaka Itakura/Alex Zahara) and his girlfriend, Kaho, from being killed in the accident at the train crossing that Makoto was originally involved in. As Makoto watches the accident in horror, time suddenly stops.
Chiaki reveals that he is a traveller from the future and leapt through time in order to see a painting being restored by Makoto's aunt, as it has been destroyed in the future. While walking in the frozen city, Chiaki hints that his original era occurs after a world wide catastrophe decimates mankind. He reveals that he has used his final leap to prevent Kōsuke's accident and has stopped time only to explain to Makoto what the consequences will be. Having revealed his origins and the source of the item that allowed Makoto to leap through time, and being unable to return to his time period, Chiaki must disappear. Makoto realizes too late that she loves him as well.
True to his words, Chiaki disappears when time begins again and Makoto is upset. As she tries to come to terms with losing him, she discovers that Chiaki's time-leap had inadvertently restored one time-leap to her: Chiaki had leapt back to before Makoto used her last leap. Makoto now leaps to the moment when she gained her powers, at which point Chiaki still has one remaining time-leap. She reveals everything that he told her in the future concerning who he is, the ability to leap through time, and his reasons for extending his stay in her time frame. Shortly before returning to his time period, Chiaki says he will wait for her in the future and Makoto replies that she will run towards it.