In Edinburgh, Scotland 1874, Jack is born on the coldest day ever. Due to the extreme cold he is born with a frozen heart which will not beat. The attendant midwife Madeleine saves his life by replacing his heart with a fragile but working cuckoo clock. She then advises him of three rules to prevent his untimely death; he must never play with the hands of the clock, he must never lose his temper, and finally he must never fall in love. Jack’s mother, for reasons known only to her, quickly decides her child would be better raised by Madeleine and departs, leaving Jack. Madeleine, incapable of bearing her own children, raises and loves him as her own.
On Jack’s tenth birthday, Madeleine repeats the three rules before taking him into town for the first time. He meets a girl in town named Miss Acacia and becomes infatuated with her. After starting school shortly afterward, he also meets Joe, a bully who is in love with Miss Acacia as well. Jealous, the older boy and his gang of students torment Jack for the next four years. During an assault from Joe, the cuckoo of Jack’s clock heart gouges Joe’s eye, and Jack runs home believing he had murdered Joe. Madeleine, believing Jack to be a fugitive, helps him to escape.
Jack only wants to see Miss Acacia again and eventually meets up with Georges Méliès, a magician attempting to operate an early film camera. Georges helps repair his heart and agrees to join Jack in the search for Miss Acacia. They proceed to Andalusia, Spain in search of her.
After a long journey they arrive at a circus in Andalusia. Jack finds Miss Acacia but Georges advises him against revealing his identity to her. He proceeds to befriend her and foolishly avoids sharing his feelings. She hints that her heart belongs to someone from her past. It turns out that Jack was that person from her past. Jack eventually finds a way to reveal himself and gives a key to Miss Acacia which can be used to wind his heart.
Before Jack and Miss Acacia could run away together, Joe, the bully from Jack’s past, shows up. He had been looking for an opportunity to further punish Jack and explains to her the three rules of Jack’s cuckoo clock heart in an attempt to sabotage them. Miss Acacia, after talking with Joe, decides she doesn’t want to risk being the cause of death of Jack by allowing him to fall in love. She rejects him, and leaves with Joe. Jack, after being rejected, tears at the screws of his heart.
In the carriage with Miss Acacia and Joe, he tells her that soon after Jack escaped with Madeleine’s help, Madeleine was sent to prison. There, she died soon afterwards. Rumors said that she died of a broken heart. Miss Acacia eventually realizes she holds the key to Jack’s survival and returns to search for him. She finds out quickly Jack had departed for home in Edinburgh and follows behind him. She knows she has only a short time to reach him. When he reached home, he is told what happened to Madeleine. They also tell him that Jack gave her the joy of being a mother and she worried at the thought of how he will grow up.
Miss Acacia finds Jack in front of Madeleine’s grave, shivering in the cold. She tries to use the key to turn his clock but he throws away the key, choosing love over life. Then they finally kiss. When Jack breaks the kiss, time has stopped. Jack sings a song about climbing to Heaven while using the frozen snowflakes as a ladder, ascending into the sky as the film fades to black.