Fowles was born in Leigh-on-Sea in Essex, England, the son of Gladys May Richards and Robert John Fowles. Robert Fowles came from a family of middle-class merchants of London. Robert's father Reginald was a partner of the firm Allen & Wright, a tobacco importer. Robert's mother died when he was six years old. At the age of 26, after receiving legal training, Robert enlisted in the Honourable Artillery Company and spent three years in the trenches of Flanders during the First World War. Robert's brother Jack died in the war, leaving a widow and three children. During 1920, the year Robert was demobilised, his father Reginald died. Robert became responsible for five young half-siblings as well as the children of his brother. Although he had hoped to practise law, the obligation of raising an extended family forced him into the family trade of tobacco importing.
Gladys Richards belonged to an Essex family also originally from London. The Richards family moved to Westcliff-on-Sea in 1918, as Spanish flu swept through Europe, for Essex was said to have a healthy climate. Robert met Gladys Richards at a tennis club in Westcliff-on-Sea in 1924. Though she was ten years younger, and he in bad health from the war, they were married a year later on 18 June 1925. Nine months and two weeks later, Gladys gave birth to John Robert Fowles.
In 1939, Fowles won a place at Bedford School, a two-hour train journey north of his home. His time at Bedford coincided with the Second World War. Fowles was a student at Bedford until 1944. He became head boy and was an athletic standout: a member of the rugby-football third team, the fives first team, and captain of the cricket team, for which he was a Bowler.
After completing his military Service in 1947, Fowles entered New College, Oxford, where he studied both French and German, although he stopped studying German and concentrated on French for his BA. Fowles was undergoing a political transformation. Upon leaving the marines, he wrote, "I ... began to hate what I was becoming in life—a British Establishment young hopeful. I decided instead to become a sort of anarchist."
Fowles composed a number of poems and short stories throughout his life, most of which were lost or destroyed. In December 1950 he wrote My Kingdom for a Corkscrew. For A Casebook (1955) was rejected by various magazines. In 1970 he wrote The Last Chapter.
In 1951, Fowles became an English master at the Anargyrios and Korgialenios School of Spetses on the Peloponnesian island of Spetses (also known as Spetsai). This opened a critical period in his life, as the island was where he met his Future wife Elizabeth Christy, née Whitton, wife of fellow Teacher Roy Christy. Inspired by his experiences and feelings there, he used it as the setting of his novel, The Magus (1966). Fowles was happy in Greece, especially outside the school. He wrote poems that he later published, and became close to his fellow expatriates. But during 1953, Fowles and the other masters at the school were all dismissed for trying to institute reforms, and Fowles returned to England.
His separation from Elizabeth did not last long. On 2 April 1957, they were married. Fowles became stepfather to Elizabeth's daughter from her first marriage, Anna. For nearly ten years, Fowles taught English as a foreign language to students from other countries at St. Godric's College, an all-girls establishment in Hampstead, London.
In late 1960, though he had already drafted The Magus, Fowles began working on The Collector. He finished his first draft in a month, but spent more than a year making revisions before showing it to his agent. Michael S. Howard, the publisher at Jonathan Cape was enthusiastic about the manuscript. The book was published in 1963 and when the paperback rights were sold in the spring of that year, it was "probably the highest price that had hitherto been paid for a first novel," according to Howard. British reviewers found the novel to be an innovative thriller, but several American critics detected a serious promotion of existentialist thought.
In 1965 Fowles left London, moving to Underhill, a farm in Dorset. The isolated farm house became the model for The Dairy in the book Fowles was writing: The French Lieutenant's Woman (1969). Finding the farm too remote, as "total solitude gets a bit monotonous," Fowles remarked, in 1968 he and his wife moved to Lyme Regis in Dorset. They lived much of the time in Belmont (formerly owned by Eleanor Coade), which Fowles used as a setting for parts of The French Lieutenant's Woman. In this novel, Fowles created one of most enigmatic female characters in literary history. His conception of femininity and myth of masculinity as developed in this text is psychoanalytically informed.
In the same year, he adapted The Magus for cinema, and the film was released in 1968. The film version of The Magus (1968) was generally considered awful; when Woody Allen was later asked whether he would make changes in his life if he had the opportunity to do it all over again, he jokingly replied he would do "everything exactly the same, with the exception of watching The Magus."
The French Lieutenant's Woman (1969) was released to critical and popular success. It was eventually translated into more than ten languages, and established Fowles' international reputation. It was adapted as a feature film in 1981 with a screenplay by the noted British Playwright Harold Pinter, and starring Meryl Streep and Jeremy Irons.
Fowles lived the rest of his life in Lyme Regis. His works The Ebony Tower (1974), Daniel Martin (1977), Mantissa (1981), and A Maggot (1985) were all written from Belmont House.
Joining the community, Fowles served as the curator of the Lyme Regis Museum from 1979 to 1988, retiring from the museum after having a mild stroke. Fowles was involved occasionally in politics in the town. He occasionally wrote letters to the Editor advocating preservation. Despite this involvement, he was generally considered reclusive.
In 1998, he was quoted in the New York Times Book Review as saying, "Being an atheist is a matter not of moral choice, but of human obligation."
In 1990, his first wife Elizabeth died of cancer, only a week after it was diagnosed. Her death affected him severely, and he did not write for a year. In 1998, Fowles married his second wife Sarah Smith. With Sarah by his side, Fowles died of heart failure on 5 November 2005, aged 79, in Axminster Hospital, 5 miles (8.0 km) from Lyme Regis.
In 2008, Elena van Lieshout, a former girlfriend of Fowles, presented a series of 120 love letters and postcards for auction at Sotheby's. The letters start in 1990, when Fowles was aged 65. Elena, a young Welsh admirer and a student at St. Hilda's College, Oxford, contacted the reclusive author and they developed a sensitive relationship.