Herzog was born Werner Stipetić (pronounced [stɪpɛtɪtʃ]) in Munich. He adopted his father's name Herzog, which means "duke" in German, when his father returned from a prisoner of war camp after World War II. His family moved to a remote village in Austria after the house next to theirs was destroyed during the bombing at the close of World War II. When he was 12, he and his family moved back to Munich and shared an apartment with Klaus Kinski in Elisabethstraße in Munich-Schwabing. About this, Herzog recalled, "I knew at that moment that I would be a film director and that I would direct Kinski". The same year, Herzog was told to sing in front of his class at school and he adamantly refused. He was almost expelled for this and until the age of 18 listened to no music, sang no songs and studied no instruments. He later said that he would easily give 10 years from his life to be able to play an instrument. At 14 he was inspired by an encyclopedia entry about film-making which he says provided him with "everything I needed to get myself started" as a film-maker - that, and the 35 mm camera that the young Herzog stole from the Munich Film School. He studied at the University of Munich despite earning a scholarship to Duquesne University in Pittsburgh, Pennsylvania. He supposedly dropped out in a matter of days and made his way to Mexico where he worked in a rodeo. In the early 1960s Herzog worked night shifts as a welder in a steel factory to help fund his first films.

Herzog has been married three times and has had three children. In 1967, Herzog married Martje Grohmann, with whom he had a son in 1973, Rudolph Amos Achmed. In 1980 his daughter Hanna Mattes was born to Eva Mattes. In 1987, Herzog married Christine Maria Ebenberger. Their son, Simon David Alexander Herzog, was born in 1989. In 1999 he married Lena Pisetski. They now live in Los Angeles.

Herzog's films have received considerable critical acclaim and achieved popularity on the art house circuit. They have also been the subject of controversy in regard to their themes and messages, especially the circumstances surrounding their creation. A notable example is Fitzcarraldo, in which the obsessiveness of the central character was mirrored by the director during the making of the film. His treatment of subjects has been characterized as Wagnerian in its scope, as Fitzcarraldo and his later film Invincible (2001) are directly inspired by opera, or operatic themes. He is proud of never using storyboards and often improvising large parts of the script, as he explains on the commentary track to Aguirre, The Wrath of God. Herzog directed five films starring Klaus Kinski: Aguirre, The Wrath of God, Nosferatu, Woyzeck, Fitzcarraldo, and Cobra Verde. In 1999 he directed and narrated the documentary film My Best Fiend, a retrospective on his often rocky relationship with Kinski.

Other actors who appear repeatedly in Herzog films are:

• Bruno S. in The Enigma of Kaspar Hauser and Stroszek
• Eva Mattes in Woyzeck and Stroszek
• Clemens Scheitz in The Enigma of Kaspar Hauser, Heart of Glass, Stroszek and Nosferatu the Vampyre
• José Lewgoy in Fitzcarraldo and Cobra Verde
• Brad Dourif in Scream of Stone and The Wild Blue Yonder

Chickens (against which Herzog has a phobia) are a frequent motif, appearing in:

• Game in the Sand centers around a chicken
• Signs of Life features a chicken buried up to its neck in a mound of sand
• Signs of Life and The Enigma of Kaspar Hauser feature chicken hypnosis
• Aguirre, The Wrath of God the chickens are thrown over a cliff in the open section
• Even Dwarfs Started Small features cannibalistic chickens, and several sequences of dwarfs throwing chickens
• Stroszek ends with a long shot of a dancing chicken
• Invincible features a tale about a man who thinks himself to be a rooster
• The White Diamond features a Guyanese man who adores his pet rooster and wishes to bring it up with him when offered a ride on an airship

Herzog and his films have won and been nominated for many awards over the years. Most notably, Herzog won the best director award for Fitzcarraldo at the 1982 Cannes Film Festival. Grizzly Man, directed by Herzog, won the Alfred P. Sloan Prize at the 2005 Sundance Film Festival Herzog was honored at the 49th San Francisco International Film Festival, receiving the 2006 Film Society Directing Award. Four of his films have been shown at the San Francisco International Film Festival throughout the years: Herdsmen of the Sun in 1990, Bells from the Deep in 1993, Lessons of Darkness in 1993, and Wild Blue Yonder in 2006. Herzog's April of 2007 appearance at the Ebertfest in Champaign, IL earned him the Golden Thumb Award, and an engraved glockenspiel given to him by a young film maker inspired by his films.