Runner opens with Charlie Feehan, the novel's protagonist, leaving his house on a rainy day. His mother stands on the porch and looks at the sky, discussing the black clouds with their neighbor, Mr. Redmond. While Ma believes Charlie is headed to school, he is actually entering a race to become local crime boss Squizzy Taylor's new "runner."
On his way to the race, Charlie comments that he began running in order to escape the cold that plagues the poor people of the slum in which he lives. Three months earlier, Charlie watched his father die of Spanish flu. But Charlie refuses to let the cold take him, so he runs to generate heat, simultaneously finding himself drawn to the seedy streets of Richmond.
Charlie's main competitor in the race is Jimmy Barlow, a tough and violent football player from the town of Fitzroy. While Charlie comes in second during the race, he delivers his egg unbroken, meaning he wins by a technicality. During the celebrations, Squizzy Taylor informs Charlie that he hard-boiled his egg that morning, so he knew Charlie would win.
Charlie's mother disapproves of him running packages from a known criminal, so Charlie begins a double life, earning money from Taylor while pretending to go to school. Charlie develops a sense of trust and admiration for Squizzy and his girlfriend Dolly, who is kind enough to give Charlie a new pair of boots that are much more comfortable than his father's oversized, worn-out pair. Meanwhile, Charlie strikes up a friendship with Norman Heath, a football player nicknamed "Nostrils" due to his large nose. Norman assists Charlie on a job delivering liquor across town. The boys are shocked to learn their customer is a corrupt police inspector, but Charlie embraces the sense of boldness he gets from his association with Squizzy's power.
Though Charlie normally collects scrap wood from Mr. Peacock's timber yard on Saturdays, he arrives one day to learn that Peacock will no longer allow him to take anything. Peacock tells Charlie to tell his mother that he will visit her the next day. Charlie later comes home to find Peacock kissing her neck. Charlie doesn't understand the dynamics of power and exploitation at play in the display and simply feels ashamed of his mother. After a period of estrangement from her, Charlie comes home one day to discover Peacock drunkenly abusing her in the kitchen. Peacock punches Charlie, causing Charlie to retaliate by hitting Peacock in the head with a cricket bat. Once he sees the blood pouring from the man's unconscious body, Charlie regrets not having gone for his legs. He goes to Squizzy and Dolly, who reassure Charlie. In the morning, Charlie learns that Squizzy sent men to intimidate Peacock into not causing any more trouble for Charlie.
Following the violent incident, Charlie's mother enters a state of post-traumatic stress disorder. She covers the bruises on her face with white powder and cleans the house obsessively, although she neglects Jack. Charlie begins training as a boxer with Mr. Redmond. Norman wins a football match against Barlow's team, and during the game Charlie sees a beautiful red-haired girl named Alice.
Charlie reports to work to learn Squizzy is in a bad mood after tensions with his rival, Snowy Cutmore, have escalated. Charlie collects debts for Squizzy, threatening shop owners with violent visits from Squizzy's associate Knuckles if they don't pay up. His last collection is at Alice Cornwall's father's bakery. Alice and her father cry and hold each other, saying they are unable to pay. Charlie uses three pounds of his earnings to pay off the debt himself. Having learned that Alice doesn't like boxing, Charlie quits his training. He borrows the Redmonds' gramophone and plays music for his mother. They dance together and reflect on the past.
A liquor delivery job to Fitzroy results in Norman and Charlie running into Barlow and his gang. Charlie manages to run away while Barlow catches Norman and beats him bloody. Charlie brings Norman to the hospital. When he returns home in the morning, he sees that Ma has stopped wearing face powder and has returned to her usual self. Later that day Alice Cornwall visits to thank Charlie for paying her father's debt. He learns that she likes to dance as much as his mother. Charlie visits Norman at the hospital. Though Charlie feels guilty, Norman boosts his spirits and tells him not to worry. Charlie goes to Squizzy's that night to tell him what happened on the liquor run. However, Squizzy is too busy drinking and celebrating the night's bloodshed in Fitzroy to care. Charlie returns the nice pair of boots Dolly gave him. Squizzy points a gun at Charlie's head. Charlie closes his eyes and Squizzy fires the gun at the wall. Charlie opens his eyes to see he and Squizzy are the only two standing in a room full of men—the others having ducked for cover.
Having freed himself from Squizzy's service, Charlie throws his energy into training for the Ballarat mile race and spending time with his mother, Alice, and Norman. Charlie and Mr. Redmond take a train to Ballarat, where Charlie decides he will bet the twenty-three pounds he earned from Squizzy on himself to win the race. To make his odds greater, Charlie runs the first heats barefoot. In the last race, Charlie takes first place and wins 1,200 pounds.
The novel ends with Charlie revealing to his family and friends that he has purchased a timber yard that he and Norman will run together. They retire to Charlie's house to celebrate with food, drinks, and music. Charlie and Alice dance closely together, and she sobs when she sees her father dance. As the night winds down, Charlie decides to go out for a run.