The story is told as a series of memories by Jacob Jankowski, a "ninety or ninety-three year-old" man who lives in a nursing home.
As the memories begin, Jacob Jankowski is twenty-three years old and preparing for his final exams as a Cornell University veterinary student when he receives the news that his parents were killed in a car accident. Jacob’s father was a veterinarian and Jacob had planned to join his practice. When Jacob learns that his father was deeply in debt because he had been treating animals for free as well as mortgaging the family home to provide Jacob an Ivy League education, he has a breakdown and leaves school just short of graduation. In the dark of night, he jumps on a train only to learn it is a circus train. When the owner of the circus, Uncle Al, learns of his training as a vet, he is hired to care for the circus animals. This consequently leads Jacob to share quarters with a dwarf named Walter (who is known as Kinko to the circus) and his dog Queenie. A few weeks later Jacob is summoned to take a look at Camel, an old man who, after drinking Jamaican ginger extract for many years, can't move his arms or legs. Fearing Camel will be "red-lighted" (referring to the practice of throwing circus workers off a moving train as either punishment or as severance from the circus to avoid paying wages), he hides him in his room.
The head trainer, August, is a brutal man who abuses the animals in his care (such as the new elephant Rosie) as well as the people around him. Alternately, he can be utterly charming. Jacob develops a guarded relationship with August and his wife, Marlena, with whom Jacob falls in love. August is suspicious of their relationship and beats Marlena and Jacob. Marlena subsequently leaves August and stays at a hotel while she's not performing. Uncle Al then informs Jacob that August is a paranoid schizophrenic and then utters a threat: reunite August and Marlena as a happily married couple or Walter and Camel get red-lighted.
A few days later after discovering that August has tried to see Marlena, Jacob visits her in her hotel room. Soon after he comforts her however, the couple sleeps together and then eventually declares their love for each other. Marlena soon returns to the circus to perform (and also to have secret meetings with Jacob), but refuses to have August near her, which makes Uncle Al furious. Days later Marlena informs Jacob that she is pregnant.
One night Jacob climbs up and jumps each car, while the train is moving, to August's room, carrying a knife between his teeth intending to kill August. However, Jacob backs out and returns to his car, only to find no one there but Queenie. He then realizes that Walter and Camel were red-lighted and Jacob himself was supposed to be too.
As the story climaxes, several circus workers who were red-lighted off the train come back and release the animals causing a stampede during the performance.
In the ensuing panic, August is killed by Rosie the elephant, and the only one who sees the incident is Jacob. As a result of this incident, which occurred during a circus performance, the circus is shut down. Soon after, Uncle Al's body is found with a makeshift garrote around his neck. Marlena and Jacob leave, along with several circus animals, and begin their life together.
Ninety-three year old Jacob is waiting for his family to take him to the circus. It is revealed that Jacob and Marlena married and had 5 children spending the first 7 years at another circus before Jacob got a job as a vet for the zoo. Marlena is revealed to have died a few years before Jacob was put into a nursing home. After finding out no one is coming for him, elderly Jacob goes to the circus on his own. He soon meets the manager Charlie and begs him to accompany the circus by selling tickets. Charlie agrees and Jacob believes he has finally come home.