John, Lord Clayton (Paul Geoffrey), the heir to the 6th Earl of Greystoke, and his pregnant wife Alice (Cheryl Campbell) are shipwrecked on the African coast. John builds a home in the trees, and Alice gives birth to a son. Alice later grows ill from malaria and dies. While John is grieving her, the tree house is visited by curious great apes, and he is killed by one of the apes. One female of the group, Kala, who is carrying her dead infant, hears the cries of the infant human in his crib. She adopts the boy and raises him as a member of the Mangani.
At age five, the boy (Danny Potts) is still trying to fit in with his ape family. When a black panther attacks, he learns how to swim to evade it while another ape is killed.
At age 12, the boy (Eric Langlois) discovers the tree-house in which he lived as a baby with his mother and father. He finds a wooden block, with pictures of both a boy and a chimpanzee painted on it. He sees himself in a mirror and recognizes the physical differences between himself and the rest of his ape family. He also discovers his father's hunting knife and how it works. The objects fascinate the boy, and he takes them with him. One day his mother is killed by a native hunting party, and he kills one of their number in revenge.
Years later, Belgian explorer Philippe d'Arnot (Ian Holm) is traveling with a band of British adventurers along the river. He is disgusted by their boorish nature and love of 'blood and sport'. A band of natives attack the party, killing everyone except Philippe, who is injured and conceals himself in the trees. The young man (Christopher Lambert) finds Philippe and nurses him back to health. D'Arnot discovers that the man is a natural mimic and teaches him to speak rudimentary English. D'Arnot deduces that this man is the son of the late Lord John and Lady Alice of Greystoke and calls the man "Jean" (the French version of John). Jean agrees to return to England with his benefactor and reunite with his human family.
On arrival at Greystoke, the family's country estate in the Lowlands of Scotland, John is welcomed by his grandfather, the 6th Earl of Greystoke (Sir Ralph Richardson), and his ward, a young American woman called Jane (played by Andie MacDowell and voiced by Glenn Close). The Earl still grieves the loss of his son and daughter-in-law years earlier but is very happy to have his grandson home. He displays eccentric behaviour and often confuses John with John's father.
John is treated as a novelty by the local social set, and some of his behaviour is seen as threatening and savage. He befriends a young mentally disabled worker on the estate and in his company relaxes into his natural ape-like behavior. Jane meanwhile teaches John more English, French, and social skills. They become very close and one evening have sex secretly.
Lord Greystoke enjoys renewed vigour at the return of his grandson and, reminiscing about his childhood game of using a silver tray as a toboggan on a flight of stairs in the grand house, decides to relive the old pastime. He crashes at the foot of the stairs and slowly dies, apparently from a head injury, in the arms of his grandson. At his passing, John displays similar emotion and lack of understanding about death as he did in Africa following the death of Kala.
John inherits the title Earl of Greystoke. Jane helps John through his grief, and they become engaged. He is also cheered when his mentor, Philippe, returns. One day he visits the Natural History Museum in London with Jane. During their visit, John is disturbed by the displays of stuffed animals. He discovers many live, caged apes from Africa, including his adoptive father, Kerchak. They recognise each other, and John releases Kerchak and other caged animals. They are pursued by police and museum officials. They reach a woodland park, where Kerchak is fatally shot. John, devastated, yells to the crowd, "He was my father!"
Unable to assimilate to the human society that he views as cruel, John decides to return to Africa and reunite with his ape family. Philippe and Jane escort him back to the jungle where Philippe and John first met. John returns to the world he understands. Jane does not join him, but Philippe expresses his hope that perhaps they may someday be reunited.
