Born in Bourg-Argental, Loire, Guyotat wrote his first novel, Sur un cheval, in 1960. He was called to Algeria in the same year. In 1962 he was found guilty of desertion and publishing forbidden material. After three months in jail he was transferred to a disciplinary centre. Back in Paris, he got involved in journalism, writing first for France Observateur, then for Nouvel Observateur. In 1964, Guyotat published his second novel Ashby.

In 1967, he published Tombeau pour cinq cent mille soldats (later released in English as Tomb for 500,000 Soldiers). Based on Guyotat's ordeal as a soldier in the Algerian War, the book earned a cult reputation and became the subject of various controversies, mostly because of its omnipresent sexual obsessions and homoeroticism.

In 1968, Guyotat became a member of the French Communist Party, which he left in 1971.

Eden, Eden, Eden came out in 1970 with a preface by Michel Leiris, Roland Barthes and Philippe Sollers (Michel Foucault's text was received late and therefore didn't appear as a preface). This book was banned from being publicized or sold to under-18s. A petition of international support was signed (notably by Pier Paolo Pasolini, Jean-Paul Sartre, Pierre Boulez, Joseph Beuys, Pierre Dac, Jean Genet, Simone de Beauvoir, Joseph Kessel, Maurice Blanchot, Max Ernst, Italo Calvino, Jacques Monod, and Nathalie Sarraute). François Mitterrand, and Georges Pompidou tried to get the ban lifted but failed. Claude Simon (who won the Nobel Prize in 1985) resigned from the jury of the Prix Médicis after the prize wasn't awarded to Eden, Eden, Eden.