In September 1939, the United Kingdom declares war on Nazi Germany, and children are evacuated from London to the countryside for their safety. Tom Oakley, a lonely and bitter old man living in the countryside village of Little Weirwold, is forced to look after one of the evacuees, William "Willie" Beech. Tom has become reclusive after losing his wife and child to scarlet fever many years before, while Willie is a quiet young boy who comes from an abusive home and is apprehensive of Tom.

Despite initial difficulties combined with his reluctance to care for Willie, Tom later takes pity on Willie after learning about his abusive upbringing by discovering the leather belt his mother used to beat him, which he throws into the garden, and does his best to create a suitable home for Willie, such as providing him with new clothes and helping to educate him. Willie's new life with Tom eventually boosts his self-confidence and he opens up to Tom, looking up to him as a surrogate father figure. He also meets and becomes best friends with a Jewish boy, Zacharias "Zach" Wrench. However, shortly after Willie's tenth birthday, Tom receives a letter from Mrs. Beech, who claims to be ill and needs Willie back in London to look after her.

When Willie reunites with his mother, he discovers that she lied to get him to return and is completely fine. Willie also meets his baby half-sister, Trudy. Mrs. Beech claims she is a "present from Jesus", but Willie is too young and naïve to consider any other scenario. It is obvious, however, that Mrs. Beech has been made much more uneasy by the Blitz, and after an argument sparked by her discovery of the absence of the belt, she sends Willie to his room for the night. The next day, Mrs. Beech seems better after suffering a mental breakdown, but when Willie presents her with gifts that the locals from Little Weirwold had given him, and tells her about some of his friends, she accuses him of stealing and is angry he had been interacting with girls and Jews. She finally pummels him and eventually locks him in the cupboard under the stairs, accusing him of blasphemy after he tells her that Jesus was a Jew. Back in Little Weirwold, Tom starts missing Willie greatly. Initially, he thinks Willie has moved on from him, until he digs up the belt in the garden. Tom has an instinct that Willie is in danger, and travels to London with his dog, Sammy.

After spending the night in an air raid shelter, Tom enlists the help of an A.R.P. Warden, Ralph, to find Willie's address. They are informed by a neighbour, unaware that Willie has returned from evacuation, that Mrs. Beech has left. Sammy detects a strange smell from the house and Tom breaks the door down. Sammy leads Tom and Ralph to the cupboard under the stairs, which appears to be the source of a vile stench. They find Willie bloodied and battered, but still alive, and chained to the closet wall. He is also holding Trudy, who has died. Tom visits Willie in the hospital and meets Dr. Stelton, a child psychiatrist who works with a children's home in Sussex. Stelton wishes to take Willie to the children's home as he believes he needs psychiatric treatment, although he promises to attempt to trace any surviving relatives that Willie might have. It is during a discussion with Ralph that Tom learns about Willie's early childhood; Willie's father was a violent wife-beating alcoholic who choked to death on his own vomit. Tom decides that it would be best for Willie to return to Little Weirwold and kidnaps him from the hospital.

Willie gradually recovers from his injuries and reunites with Zach and the others. While speaking with Zach, Willie learns about the concept of sex, something his mother raised him to believe was "something dirty" and unacceptable, and realises that his mother herself had been having a relationship with another man, which resulted in the birth of Trudy. Eventually, Stelton and some social workers come to Tom's house with the news that Willie's mother has died by suicide. They intend to take Willie to the children's home, but Willie and Tom protest. Tom explains a bad dream that Willie has repeatedly been having regarding this exact event, and argues that he needs to be with someone who loves him.

Tom speaks alone with an official from the Home Office, Mr. Greenway, and persuades him that the only reason he wants Willie back is because he loves him like his own son and that Willie has clearly been happier with him than he ever was when he lived with his mother. Mr. Greenway accepts Tom's story and allows him to adopt Willie. Unfortunately, Willie's newfound happiness is cut short when Zach receives a phone call from his mother, saying that London's East End was bombed while his father was there. Willie sees Zach just before he leaves for London and bids him goodbye.

Willie dreams soon after that he and Mr Tom are asleep in an air raid shelter. The next morning at breakfast, he is informed that Zach was killed in another air raid. The news devastates Willie, causing him to withdraw from everyone. Tom however, remembers how he felt when he lost his own family, and in order to stop Willie going down the same path he did, gives Willie a heartfelt speech that while a loved one may physically be gone, they will always live on inside his mind and heart, which can never be taken away.

Willie eventually overcomes his grief and teaches himself how to ride the bicycle Zach left behind. In the film's final scene, Willie rides the bicycle down the long hill and stops just in front of an impressed Tom, whom he addresses as "Dad" for the first time.

• John Thaw as Tom Oakley
• Nick Robinson as William Beech
• Annabelle Apsion as Mrs Beech
• Thomas Orange as Zacharias Wrench
• William Armstrong as Dr Stelton
• Geoffrey Beevers as Vicar
• Mossie Smith as Mrs Fletcher
• Peter England as Michael Fletcher
• Ivan Berry as George Fletcher
• Harry Capehorn as Edward Fletcher
• Merelina Kendall as Mrs Holland
• Geoffrey Hutchings as ARP Warden Ralph
• Marlene Sidaway as Mrs Webster
• John Cater as Dr Little
• Denyse Alexander as Mrs Little
• Avril Elgar as Mrs Ford
• Pauline Turner as Annie Hartridge

• National Television Awards 1999: Best Drama for Goodnight Mister Tom
• BAFTA 1999: Lew Grade Award for Most Popular Television Programme of 1998 for Goodnight Mister Tom
• Television & Radio Industries Club Award 1999: Best ITV/Channel 5 Programme of 1998 for Goodnight Mister Tom

• Goodnight Mister Tom at IMDb