Djerassi hailed from a Jewish family, as the son of Alice Friedmann, an Ashkenazi Viennese Jew with roots in Galicia, and Samuel Djerassi, a Bulgarian Sephardic Jew. Following his parents' divorce, Djerassi and his mother moved to Vienna to take advantage of the better school system. Until age fourteen, he attended the same realgymnasium that Sigmund Freud had attended many years earlier; he spent summers in Bulgaria with his father. After the Anschluss, his father briefly remarried his mother in 1938 to allow Carl to escape the Nazi regime and flee to Bulgaria, where he lived with his father for a year. Djerassi's father was a physician who specialized in treating syphilis with the existing arsenical drugs. His successful practice in Sofia was limited to a few wealthy patients, whose treatment lasted for years. A few years later, Djerassi arrived with his mother in the United States, nearly penniless...they had only $20 between them, which was swindled from them by a cab driver. Djerassi's mother worked in a group practice in upstate New York. In 1949, his father also emigrated to the United States and eventually settled near his son in San Francisco.

Djerassi briefly attended Tarkio College, now defunct, then studied chemistry at Kenyon College, which is famous for literary criticism and the Kenyon Review but not known for chemistry. He graduated summa cum laude, then got his PhD at the University of Wisconsin. He worked for CIBA in New Jersey, developing Pyribenzamine (tripelenamine), his first patent and the first commercial antihistamine.

In 1949, Djerassi was recruited to be the associate director of research at Syntex in Mexico City by then-technical director George Rosenkranz, working there from 1950-1951. At Syntex, he worked on a new synthesis of cortisone based on diosgenin, a steroid sapogenin derived from a Mexican wild yam. His team later synthesized norethindrone, a progestin-analogue that was effective when taken by mouth. This became part of the first successful oral contraceptive, the combined oral contraceptive pill (COCP). COCPs became known colloquially as the birth-control pill, or simply, the Pill.

In 1959, Djerassi became a professor of chemistry at Stanford University and the president of Syntex Laboratories in Mexico City and Palo Alto, California. The Syntex connection made Djerassi a rich man. He bought a large tract of land in Woodside, California, started a cattle ranch, and also built up a large art collection. He started a new company, Zoecon, which focused on pest control without insecticides, using modified insect growth hormones to stop insects from metamorphosing from the larval stage to the pupal and adult stages. He sold Zoecon to Occidental Petroleum, which later sold it to Sandoz. Part of Zoecon lingers in Dallas, Texas, making products to control fleas and other pests.

On July 5, 1978, Djerassi's daughter Pamela, an artist, killed herself. Djerassi considered how he could help living artists, rather than collecting dead ones. He donated his Klee collection to the San Francisco Museum of Modern Art, effectiive on his death.He visited existing artist's colonies, such as Yaddo and McDowell, and decided to create his own. He closed down his cattle ranch, converted the barn and the houses to residential and work space for a number of artists of many kinds, brought in a prize-winning chef, and moved to an office building he had renovated in San Francisco, converting one floor into a posh apartment, where he displayed part of his art collection and hosted a literary salon). He hung up his lab coat and became an emeritus professor.

In 1992 he was awarded the Priestley Medal. Austria has issued a postage stamp with Djerassi's picture on it. The Austrian government also sent him a new Austrian passport. He was awarded the Austrian Cross of Honor for Art and Science, First Class, in 1999.

Djerassi perceived the pill as having a huge impact on the social processes of women and men, which to a significant extent is influenced through the sociobiology of sexual reproduction. He anticipated a far greater social impact on men than on women, in what he called as the feminization of men, implying the "social-feminization" of laws and social values in favor of women in society as a whole.

In 1973, Djerassi was awarded the National Medal of Science by President Nixon for his work on the Pill which was ironic to a degree, as he reported in his memoir, his name at the time was on the infamous "Nixon's enemies list", which was compiled by Charles Colson and Nixon. He learned this from an article in the San Francisco Examiner, several months later.

In 1975 he was awarded the Perkin Medal.

In 1978, he was inducted into the National Inventors Hall of Fame. In 1991, he was awarded the National Medal of Technology for "his broad technological contributions to solving environmental problems; and for his initiatives in developing novel, practical approaches to insect control products that are biodegradable and harmless."

In 1992 he was awarded the Priestley Medal.

Austria has issued a postage stamp with Djerassi's picture on it. The Austrian government also sent him a new Austrian passport. He was awarded the Austrian Cross of Honor for Art and Science, First Class, in 1999.

Djerassi is a member of the Board of Sponsors of the Bulletin of the Atomic Scientists and is chairman of the Pharmanex Scientific Advisory Board.

Djerassi Glacier on Brabant Island in Antarctica is named after Carl Djerassi.

In 2009 awarded the Alecrin Prize in Vigo (Spain).

Non-fiction

• Optical Rotatory Dispersion, McGraw-Hill & Company, 1960.
• The Politics of Contraception, W H Freeman & Company, 1981, ISBN 0-7167-1342-X
• Steroids Made it Possible (Profiles, Pathways, and Dreams), American Chemical Society, 1990, ISBN 0-8412-1773-4 (autobiography)
• The Pill, Pygmy Chimps, and Degas' Horse, Basic Books, 1992, ISBN 0-465-05758-6 (autobiography)
• From the Lab into The World: A Pill for People, Pets, and Bugs, American Chemical Society, 1994, ISBN 0-8412-2808-6
• Paul Klee: Masterpieces of the Djerassi Collection, (coeditor), Prestel Publishing, 2002, ISBN 3-7913-2779-8
• Dalla pillola alla penna, Di Renzo Editore, 2004, ISBN 8883230868
• This Man's Pill: Reflections on the 50th Birthday of the Pill , Oxford University Press, USA, 2004, ISBN 0-19-860695-8 (autobiography)

Fiction

• Futurist and Other Stories, Macdonald, 1989, ISBN 0-356-17500-6
• The Clock Runs Backwards, Story Line Press, 1991, ISBN 0-934257-75-2
• Marx, Deceased, University of Georgia Press, 1996, ISBN 0-8203-1835-3

Science-in-fiction

Djerassi describes some of his novels as "science-in-fiction" - fiction which portrays the lives of real scientists, with all their accomplishments, conflicts, and aspirations. The genre is also referred to as Lab lit.

• Cantor's Dilemma, Penguin, 1989, ISBN 0-14-014359-9
• The Bourbaki Gambit, Penguin, 1994, ISBN 0-14-025485-4
• Menachem's Seed, Penguin, 1996, ISBN 0-14-027794-3
• NO, Penguin, 1998, ISBN 0-14-029654-9

Drama

• An Immaculate Misconception: Sex in an Age of Mechanical Reproduction, Imperial College Press, 2000, ISBN 1-86094-248-2 (adapted from the novel Menachem's Seed)
• L.A. Theatre Works, Audio Theatre Collection CD, 2004, ISBN 1-58081-286-4
• Oxygen, Wiley-VCH, (with Roald Hoffmann, coauthor), 2001, ISBN 3-527-30413-4
• Newton's Darkness: Two Dramatic Views, (with David Pinner, coauthor), Imperial College Press, 2004, ISBN 1-86094-390-X
• Four Jews on Parnassus