• Signs of Life (1968)
• Even Dwarfs Started Small (1970)
• Aguirre, the Wrath of God (1972)
• The Enigma of Kaspar Hauser (1974)
• Heart of Glass (1976)
• Stroszek (1977)
• Nosferatu the Vampyre (1979)
• Woyzeck (1979)
• Fitzcarraldo (1982)
• Where the Green Ants Dream (1984)
• Cobra Verde (1987)
• Scream of Stone (1991)
• Invincible (2001)
• The Wild Blue Yonder (2005)
• Rescue Dawn (2006)
• Bad Lieutenant: Port of Call New Orleans (2009)
• My Son, My Son, What Have Ye Done? (2009)
• Queen of the Desert (2015)
• Salt and Fire (2016)

• Herakles (1962)
• Game in the Sand (1964)
• The Unprecedented Defence of the Fortress Deutschkreuz (1966)
• Last Words (1968)
• Precautions Against Fanatics (1969)
• No One Will Play with Me (1976)
• Les Gaulois (1988)

• The Flying Doctors of East Africa (1969)
• Handicapped Future (1971)
• Land of Silence and Darkness (1971)
• Fata Morgana (1971)
• The Great Ecstasy of Woodcarver Steiner (1974)
• How Much Wood Would a Woodchuck Chuck (1976)
• Huie's Sermon (1981)
• God's Angry Man (1981)
• Ballad of the Little Soldier (1984)
• The Dark Glow of the Mountains (1984)
• Herdsmen of the Sun (1989)
• Echoes from a Sombre Empire (1990)
• Jag Mandir (1991)
• Lessons of Darkness (1992)
• Bells from the Deep (1993)
• The Transformation of the World into Music (1994)
• Gesualdo: Death for Five Voices (1995)
• Little Dieter Needs to Fly (1997)
• Wings of Hope (1998)
• My Best Fiend (1999)
• Wheel of Time (2003)
• The White Diamond (2004)
• Grizzly Man (2005)
• Encounters at the End of the World (2007)
• Cave of Forgotten Dreams (2010)
• Happy People: A Year in the Taiga (2010)
• Into the Abyss (2011)
• Lo & Behold, Reveries of the Connected World (2016)
• Into the Inferno (2016)

• La Soufrière (1977)
• Portrait Werner Herzog (1986)
• Christ and Demons in New Spain (1999)
• Pilgrimage (2001)
• Ten Thousand Years Older (2002)
• La Bohème (2009)
• Ode to the Dawn of Man (2011)
• From One Second to the Next (2013)

• On Death Row (2012-2013, 8 Episodes)
• Filmstunde (1991-1992, 4 Episodes)

Films written, not directed, by Herzog:

• Werner Herzog Eats His Shoe (1980)

Herzog has written all his films, except these which he co-wrote:

• Heart of Glass (1976)
• Scream of Stone (1991)
• Bad Lieutenant: Port of Call New Orleans (2009)
• My Son, My Son, What Have Ye Done? (2009)

Herzog has also co-written:

• Hunger in the world explained to my son (El hambre en el mundo explicada a mi hijo) (2002)
• Incident at Loch Ness (2004)
• Happy People: A Year in the Taiga (2010)

• Geschichten vom Kübelkind (1971)
• Man of Flowers (1983)
• Bride of the Orient (1989)
• Hard to Be a God (1990)
• Tales from the Opera (1994)
• Burning Heart (1995)
• What Dreams May Come (1998)
• Julien Donkey-Boy (1999)
• Incident at Loch Ness (2004)
• Mister Lonely (2007)
• The Grand (2007)
• Plastic Bag (2009)
• The Boondocks (Season 3) Ep. 31: "It's a Black President, Huey Freeman" (air date May 2, 2010) – voice role
• The Simpsons Ep. 479 (2011) – voice role
• Metalocalypse (Season 4, recurring character) (2012) – voice role
• American Dad! Ep. 132 (2012) – voice role
• Dinotasia (2012) – narrator
• Jack Reacher (2012)
• Home from Home (2013)
• The Wind Rises (English version) (2013) – voice role
• Penguins of Madagascar (2014) – voice role
• Parks and Recreation (2015)
• Rick and Morty Season 2 Ep. 8: "Interdimensional Cable 2: Tempting Fate" (2015) – voice role

• A Gray State (2017)