Werner Nekes grew up in Duisburg-Hamborn, and went to school in Oberhausen and in Mülheim/Ruhr. In 1963, he started to study linguistics and psychology in Freiburg and from 1964 on in Bonn where he was the head of the student film club. From 1965 on, Nekes made his first experimental films, at first on 8mm, then on 16mm film. He then met the painter Dore O. and followed her to Hamburg in 1967 where they got married. In the following year, Nekes co-founded Filmmacher-Cooperative and Hamburger Filmschau. He also did public film screenings in his apartment.

In 1968, Nekes won his first international film award in Sao Paulo for his short experimental film "schwarzhuhnbraunhuhnschwarz-huhnweißhuhnrothuhnweiß oder put-putt". One year later, he received a "Bambi" award for his complete works and in 1970, he won a Filmband in Silber for "jüm-jüm" (1967). This ten-minute film shows Dore O., who besides her own experimental film oeuvre participated in most of Nekes' films, sitting on a swing and moving back and forth in front of painted oversized phallus, while the motion sequence was newly organized by mathematically structured editing.

With the silent film "Kelek" (1968), Nekes turned movie goers into voyeurs who are looking out of a trellised basement window and are observing passing pedestrians. From 1970 to 1972, Nekes was a professor for experimental film at Hamburg's Hochschule für bildende Künste. In the summer of 1978, Nekes and Dore O. returned to Mülheim/Ruhr where they live until today. From 1982 to 1984, Nekes was a professor at Offenbach's art college.

His ambitious principal work is the film collage "Uliisses" (1980 to 1982), filmed in English, that links Homer's "Odyssey" with James Joyce's "Ulysses", while incorporating scenes from the 24-hour play "The Warp" by the British science fiction writer Neil Oram and from the Essen-based photographer Uli. Nekes used most different film techniques, took apart film rolls, used computerized aperture shutters, laser beams, and holographic images, and resorted to old cinematographic techniques of prehistory and early history, like the Polyorama panoptique or old optical toys. The film won numerous awards. As homage to Karl Valentin and Liesl Karlstadt, Nekes finished the grotesque music film "Johnny Flash", starring the comedian Helge Schneider who had already written the score for "Uliisses". In "Johnny Flash", Schneider played the clumsy electrician Jürgen who lives in the Ruhr area and dreams about a career as a pop singer.

Nekes, a versatile collector of historic optical objects from the prehistory and early history of the cinema, presented parts of his collection in "Was geschah wirklich zwischen den Bildern?" ("Film Before Film", 1985) and in the four-part TV documentary "Media Magica" (1995/96). With the experimental-erotic film "Der Tag des Malers" ("The Day of the Painter"), Nekes filmed artistic abstractions of nude models in a pictorial approach to Matisse, Duchamp, and Dürer.

In 2004 and again in 2006, Nekes was a guest professor at the University of Fine Arts of Hamburg. In 2009, he was accepted into the class of the arts of the North Rhine-Westphalian Academy of Sciences, Humanities and the Arts. Between 2008 and 2011 he made several more experimental short films.

Werner Nekes passed away on January 22, 2017.