Jodorowsky was born in 1929 in the coastal town of Tocopilla, Chile, to parents who were Jewish immigrants from Yekaterinoslav (now Dnipro), Elisavetgrad (now Kropyvnytskyi) and other cities of the Russian Empire (now Ukraine). His father, Jaime Jodorowsky Groismann, was a merchant, who was largely abusive to his wife Sara Felicidad Prullansky Arcavi, and at one time accused her of flirting with a customer. Angered, he subsequently beat and raped her, getting her pregnant, which led to the birth of Alejandro. Because of this brutal conception, Sara both hated her husband and disliked her son, telling him that “I cannot love you” and rarely showing him tenderness. Alejandro also had an elder sister, Raquel Jodorowsky, but disliked her, for he believed that she was selfish, doing “everything to expel me from the family so that she could be the centre of attention.” Alongside his dislike for his family, he also held contempt for many of the local people, who viewed him as an outsider because of his status as the son of immigrants, and also for the American mining industrialists who worked locally and treated the Chilean people badly. It was this treatment at the hands of Americans that led to his later condemnation of American imperialism and neo-colonialism in Latin America in several of his films. Nonetheless he liked his local area, and was greatly unhappy when he was forced to leave it at the age of nine years old, something for which he blamed his father. His family subsequently moved to the city of Santiago, Chile.

Born to Jewish-Ukrainian parents in Chile, Jodorowsky experienced an unhappy and alienated childhood, and so immersed himself in reading and writing poetry. Dropping out of college, he became involved in theater and in particular mime, working as a clown before founding his own theater troupe, the Teatro Mimico, in 1947. Moving to Paris in the early 1950s, Jodorowsky studied mime under Étienne Decroux before turning to cinema, directing the short film Les têtes interverties in 1957. From 1960 he divided his time between Paris and Mexico City, in the former becoming a founding member of the anarchistic avant-garde Panic Movement of performance artists. In 1966 he created his first comic strip, Anibal 5, while in 1967 he directed his first feature film, the surrealist Fando y Lis, which caused a huge scandal in Mexico, eventually being banned.

He immersed himself in reading, and also began writing poetry, having his first poem published when he was sixteen years old, alongside associating with such Chilean poets as Nicanor Parra, Stella Díaz Varín and Enrique Lihn. Becoming interested in the political ideology of anarchism, he began attending college, studying psychology and philosophy, but stayed for only two years. After dropping out, and having an interest in theatre and particularly mime, he took up employment as a clown in a circus and began a career as a theatre director. Meanwhile, in 1947 he founded his own theatrical troupe, the Teatro Mimico, which by 1952 had fifty members, and the following year he wrote his first play, El Minotaura (The Minotaur). Nonetheless, Jodorowsky felt that there was little for him left in Chile, and so that year he moved to Paris, France.

It was while in Paris that Jodorowsky began studying mime with Étienne Decroux and joined the troupe of one of Decroux’s students, Marcel Marceau. It was with Marceau’s troupe that he went on a world tour, and wrote several routines for the group, including “The Cage” and “The Mask Maker”. After this, he returned to theatre directing, working on the music hall comeback of Maurice Chevalier in Paris. In 1957, Jodorowsky turned his hand to filmmaking, creating Les têtes interverties (The Severed Heads), a 20-minute adaptation of Thomas Mann’s novella. It consisted almost entirely of mime, and told the surreal story of a head-swapping merchant who helps a young man find courtship success. Jodorowsky played the lead role. The director Jean Cocteau admired the film, and wrote an introduction for it. It was considered lost until a print of the film was discovered in 2006.

In 1960, Jodorowsky moved to Mexico, where he settled down in Mexico City. Nonetheless, he continued to return occasionally to France, on one occasion visiting the Surrealist artist André Breton, but he was disillusioned in that he felt Breton had become somewhat conservative in his old age. Continuing his interest in surrealism, in 1962 he founded the Panic Movement along with Fernando Arrabal and Roland Topor. The movement aimed to go beyond the conventional surrealist ideas by embracing absurdism. Its members refused to take themselves seriously, while laughing at those critics who did. In 1966 he produced his first comic strip, Anibal 5, which was related to the Panic Movement. The following year he created a new feature film, Fando y Lis, loosely based on a play written by Fernando Arrabal, who was working with Jodorowsky on performance art at the time. Fando y Lis premiered at the 1968 Acapulco Film Festival, where it instigated a riot amongst those objecting to the film’s content, and subsequently it was banned in Mexico.

It was in Mexico City that he encountered Ejo Takata (1928–1997), a Zen Buddhist monk who had studied at the Horyuji and Shofukuji monasteries in Japan before traveling to Mexico via the United States in 1967 to spread Zen. Jodorowsky became a disciple of Takata and offered his own house to be turned into a zendo. Subsequently, Takata attracted other disciples around him, who spent their time in meditation and the study of koans. Eventually, Takata instructed Jodorowsky that he had to learn more about his feminine side, and so he went and befriended the English surrealist Leonora Carrington, who had recently moved to Mexico.

In 1970, Jodorowsky released the film El Topo, which sometimes is known in English as The Mole, which he had both directed and starred in. An acid western, El Topo tells the story of a wandering Mexican bandit and gunslinger, El Topo (played by Jodorowsky), who is on a search for spiritual enlightenment, taking his young son along with him. Along the way, he violently confronts a number of other individuals, before finally being killed and being resurrected to live within a community of deformed people who are trapped inside a mountain cave. Describing the work, he stated that “I ask of film what most North Americans ask of psychedelic drugs. The difference being that when one creates a psychedelic film, he need not create a film that shows the visions of a person who has taken a pill; rather, he needs to manufacture the pill.” Knowing how Fando y Lis had caused such a scandal in Mexico, Jodorowsky decided not to release El Topo there, instead focusing on its release in other countries across the world, including Mexico’s northern neighbour, the United States. It was in New York City where the film would play as a “midnight movie” for several months at Ben Barenholtz’s Elgin Theater. It attracted the attention of rock musician and countercultural figure John Lennon, who thought very highly of it, and convinced the president of The Beatles’ company Apple Corps, Allen Klein, to distribute it in the United States.

Klein agreed to give Jodorowsky $1 million to go toward creating his next film. The result was The Holy Mountain, released in 1973. It has been suggested that The Holy Mountain may have been inspired by René Daumal’s Surrealist novel Mount Analogue. The Holy Mountain was another complex, multi-part story that featured a man credited as “The Thief” and equated with Jesus Christ, a mystical alchemist played by Jodorowsky, seven powerful business people representing seven of the planets (Venus and the six planets from Mars to Pluto), a religious training regimen of spiritual rebirth, and a quest to the top of a holy mountain for the secret of immortality. During the completion of The Holy Mountain, Jodorowsky received spiritual training from Oscar Ichazo of the Arica School, who encouraged him to take LSD and guided him through the subsequent psychedelic experience. Around the same time (2 November 1973), Jodorowsky participated in an isolation tank experiment conducted by John Lilly.

In December 1974, a French consortium led by Jean-Paul Gibon purchased the film rights to Frank Herbert’s epic 1965 science fiction novel Dune and asked Jodorowsky to direct a film version. Jodorowsky planned to cast the Surrealist artist Salvador Dalí, in what would have been his only speaking role as a film actor, in the role of Emperor Shaddam IV. Dalí agreed when Jodorowsky offered to pay him a fee of $100,000 per hour. He also planned to cast Orson Welles as Baron Vladimir Harkonnen; Welles only agreed when Jodorowsky offered to get his favourite gourmet chef to prepare his meals for him throughout the filming. The book’s protagonist, Paul Atreides, was to be played by Jodorowsky’s son, Brontis Jodorowsky. The music would be composed by Pink Floyd and Magma. Jodorowsky set up a pre-production unit in Paris consisting of Chris Foss, a British artist who designed covers for science fiction publications, Jean Giraud (Moebius), a French illustrator who created and also wrote and drew for Métal Hurlant magazine, and H. R. Giger. Frank Herbert travelled to Europe in 1976 to find that $2 million of the $9.5 million budget had already been spent in pre-production, and that Jodorowsky’s script would result in a 14-hour movie (“It was the size of a phonebook”, Herbert later recalled). Jodorowsky took creative liberties with the source material, but Herbert said that he and Jodorowsky had an amicable relationship. The production for the film collapsed when no film studio could be found willing to fund the movie to Jodorowsky’s terms. The aborted production was chronicled in the documentary Jodorowsky’s Dune. Subsequently, the rights for filming were sold to Dino de Laurentiis, who employed the American filmmaker David Lynch to direct, creating the film Dune in 1984. The documentary does not include any original film footage of what was to be Jodorowsky’s Dune but does make extraordinary claims as to the influence this unmade film had on other actual science fiction films, such as Star Wars, Alien, Terminator, Flash Gordon, and Raiders of the Lost Ark.

After the collapse of the Dune project, Jodorowsky completely changed course and, in 1980, premiered his children’s fable Tusk, shot in India. Taken from Reginald Campbell’s novel Poo Lorn of the Elephants, the film explores the soul-mate relationship between a young British woman living in India and a highly prized elephant. The film exhibited little of the director’s outlandish visual style and was never given wide release.

In 1989, Jodorowsky completed the Mexican-Italian production Santa Sangre (Holy Blood). The film received limited theatrical distribution, putting Jodorowsky back on the cultural map despite its mixed critical reviews. Santa Sangre was a surrealistic slasher film with a plot like a mix of Alfred Hitchcock’s Psycho with Robert Wiene’s The Hands of Orlac. It featured a protagonist who, as a child, saw his mother lose both her arms, and as an adult let his own arms act as hers, and so was forced to commit murders at her whim. Several of Jodorowsky’s sons were recruited as actors.

He followed in 1990 with a very different film, The Rainbow Thief. Though it gave Jodorowsky a chance to work with the “movie stars” Peter O’Toole and Omar Sharif, the executive producer, Alexander Salkind, effectively curtailed most of Jodorowsky’s artistic inclinations, threatening to fire him on the spot if anything in the script was changed (Salkind’s wife, Berta Domínguez D., wrote the screenplay).

In 1995, Alejandro’s son, Teo, died in an accident while his father was busy preparing for a trip to Mexico City to promote his new book. Upon arriving in Mexico City, he gave a lecture at the Julio Castillo Theatre where he once again met Ejo Takata, who at this time had moved into a poor suburb of the city where he had continued to teach meditation and Zen. Takata would die two years later, and Jodorowsky would never get to see his old friend again.

In 2000, Jodorowsky won the Jack Smith Lifetime Achievement Award from the Chicago Underground Film Festival (CUFF). Jodorowsky attended the festival and his films were shown, including El Topo and The Holy Mountain, which at the time had grey legal status. According to festival director Bryan Wendorf, it was an open question of whether CUFF would be allowed to show both films, or whether the police would show up and shut the festival down.

Mœbius and Jodorowsky sued Luc Besson, director of The Fifth Element, claiming that the 1997 film borrowed graphic and story elements from The Incal, but they lost their case. The suit was plagued by ambiguity since Mœbius had willingly participated in the creation of the film, having been hired by Besson as a contributing artist, but had done so without gaining the approval of Incal co-creator Jodorowsky, whose services Besson did not call upon. For more than a decade, Jodorowsky pressured his publisher Les Humanoïdes Associés to sue Luc Besson for plagiarism, but the publisher refused, fearing the inevitability of the final outcome. In a 2002 interview with the Danish comic book magazine Strip!, Jodorowsky stated that he considered it an honour that somebody stole his ideas.

In 2005, Jodorowsky officiated at the wedding of Marilyn Manson and Dita Von Teese.

Until 2007, Fando y Lis and Santa Sangre were the only Jodorowsky works available on DVD. Neither El Topo nor The Holy Mountain were available on videocassette or DVD in the United States or the United Kingdom, due to ownership disputes with distributor Allen Klein. After settlement of the dispute in 2004, however, plans to re-release Jodorowsky’s films were announced by ABKCO Films. On 19 January 2007, it was announced online that Anchor Bay would release a box set including El Topo, The Holy Mountain, and Fando y Lis on 1 May 2007. A limited edition of the set includes both the El Topo and The Holy Mountain soundtracks. And, in early February 2007, Tartan Video announced its 14 May 2007, release date for the UK PAL DVD editions of El Topo, The Holy Mountain, and the six-disc box set which, alongside the aforementioned feature films, includes the two soundtrack CDs, as well as separate DVD editions of Jodorowsky’s 1968 debut feature Fando y Lis (with his 1957 short La cravate a.k.a. Les têtes interverties, included as an extra) and the 1994 feature-length documentary La constellation Jodorowsky. Notably, Fando y Lis and La cravate were digitally restored extensively and remastered in London during late 2006, thus providing a suitable complement to the quality restoration work undertaken on El Topo and The Holy Mountain in the States by ABKCO, and ensuring that the presentation of Fando y Lis is a significant improvement over the 2001 Fantoma DVD edition. Prior to the availability of these legitimate releases, only inferior quality, optically censored, bootleg copies of both El Topo and The Holy Mountain have been circulated on the Internet and on DVD.

In an interview with Premiere Magazine, Jodorowsky said he intended his next project to be a gangster film called King Shot. In an interview with The Guardian newspaper in November 2009, however, Jodorowsky revealed that he was unable to find the funds to make King Shot, and instead would be entering preparations on Sons of El Topo, for which he claimed to have signed a contract with “some Russian producers”.

In 2010, the Museum of Arts and Design in New York City staged the first American cinema retrospective of Alejandro Jodorowsky entitled Blood into Gold: The Cinematic Alchemy of Alejandro Jodorowsky. Jodorowsky would attend the retrospective and hold a master class on art as a way of transformation. This retrospective would inspire the museum MoMA PS1 to present the exhibition Alejandro Jodorowsky: The Holy Mountain in 2011.

In August 2011, Alejandro arrived in a town in Chile where he grew up, also the setting of his autobiography The Dance of Reality, to promote an autobiographical film based upon his book.

On 31 October 2011, Halloween night, the Museum of Modern Art (New York City) honored Jodorowsky by showing The Holy Mountain. He attended and spoke about his work and life. The next evening, he presented El Topo at the Walter Reade Theatre at Lincoln Center.

Since 2011 these talks have dwindled to once a month and take place at the Librairie Les Cent Ciels in Paris.

Jodorowsky has several books on his therapeutic methods, including Psicomagia: La trampa sagrada (Psychomagic: The Sacred Trap) and his autobiography, La danza de la realidad (The Dance of Reality), which he was filming as a feature-length film in March 2012. To date he has published more than 23 novels and philosophical treatises, along with dozens of articles and interviews. His books are widely read in Spanish and French, but are for the most part unknown to English-speaking audiences.

Alejandro has stated that after finishing The Dance of Reality he was preparing to shoot his long-gestating El Topo sequel, Abel Cain. By January 2013, Alejandro finished filming on The Dance of Reality and entered into post-production. Alejandro’s son and co-star in the film, Brontis, claimed the film was to be finished by March 2013, and that the film was “very different than the other films he made”. On 23 April, it was announced that the film would have its world premiere at the Film Festival in Cannes. coinciding with The Dance of Reality premiered alongside the documentary film Jodorowsky’s Dune, which premiered in May 2013 at the Cannes Film Festival, creating a “Jodorowsky double bill”.

In 2015, Jodorowsky began a new film entitled Endless Poetry, the sequel to his last “auto-biopic”, The Dance of Reality. His Paris-based production company, Satori Films, launched two successful crowdfunding campaigns to finance the film. The Indiegogo campaign has been left open indefinitely, receiving donations from fans and movie-goers in support of the independent production. The film was shot between June and August 2015, in the streets of Matucana in Santiago, Chile, where Jodorowsky lived for a period in his life. The film portrays his young adulthood in Santiago, years during which he became a core member of the Chilean poetic avant-garde alongside artists such as Hugo Marín, Gustavo Becerra, Enrique Lihn, Stella Díaz Varín, Nicanor Parra and others. Jodorowsky’s son, Adan Jodorowsky, plays him as an adult and Brontis Jodorowsky, plays as his father Jaime. Jeremias Herskovitz, from The Dance of Reality, portrays Jodorowsky as a teenager. Pamela Flores plays as Sara (his mother) and Stella Díaz Varín (poetess and young Jodorowsky’s girlfriend). Leandro Taub portrays Jodorowsky’s best friend, the poet and novelist Enrique Lihn. The film premiered in the Directors’ Fortnight section of the Cannes Film Festival on 14 May 2016. Variety’s review was overwhelmingly positive, calling it “… the most accessible movie he has ever made, and it may also be the best.”

During an interview at the Cannes Film Festival in 2016, Jodorowsky announced his plans to finally make The Son of El Topo as soon as financial backing is obtained.

On 26 June 2017, Jodorowsky released a statement on his Facebook account in response to the question: “Did you rape an actress during the filming of El Topo?”

His film Psychomagic, a Healing Art premiered in Lyon on 3 September 2019. It was then released on streaming services on 1 August 2020.