Franz Winzentsen was born in Hamburg on January 10th, 1939. From 1959 until 1964, he attended the Hochschule für bildende Künste (hfbK) in Hamburg. Majoring in painting, graphic design and photography, his graduation project "Verfolgung" became the first film to be produced at the academy.

In 1965, Winzentsen first became an assistant, then a partner at Cinegafik, the animation studio of fellow filmmaker Helmut Herbst. There he completed several animated films, before leaving the studio in 1973. In the second half of the 1960s, Franz Winzentsen and his first wife Ursula Asher-Winzentsen were very active in Hamburg's burgeoning film community, and in 1968, they became co-founders of the  "Hamburger Filmmacher-Cooperative". He went on to produce and direct numerous animated films and essayistic shorts, including the series "Aus meinem Animationstagebuch" as well as two feature films. Following the birth of his daughter, he also made many memorable films for children.

In 1984, he won the Grand Prize at the International Animation Festival in Stuttgart for "Flamingo – aus meinem Animationstagebuch", and his short  "Die Königin des schwarzen Marktes" was the winner at the 1989 Short Film Festival Berlin. In 1987, he returned to his alma mater as a professor, and until his retirement in 2003, he taught courses in animation. In 2000, he was honoured with the "Niedersächsischer Kunstpreis Film" for his lifetime achievement as a filmmaker.

Since 1994, Franz Winzentsen has been working in his studio in Kutenholz (near Bremervörde), where he also has begun to produce object boxes and sculptures. In addition to this, he has been intensively painting since 2009. His paintings, objects and drawings have been shown in several exhibitions, including the Kunstverein Stade and the SchauRaum Hamburg-Harburg.

In addition, Winzentsen remained active as a filmmaker. His short animated film "Die so genannten Bremer Stadtmusikanten" (2009) was an idiosyncratic contribution to fairytale research; the animated film "Die Konferenz oder Die Rückseite des Mondes" (2012) was named "Short Film of the Month" by the Wiesbaden Filmbewertungsstelle (German federal authority for evaluating and rating film). The short animated films "Heimaturlaub - Aus dem Skizzenbuch eines Astronauten" (2016) and "Stampede - Eine gestempelte Geschichte vom Zirkus" (2016) were screened - like almost all of his films - at the Hamburg Short Film Festival.

In 2018, Winzentsen made the 22-minute short film "Stromausfall," in which he guides viewers through his studio during a complete blackout using only a flashlight. That same year, he became a member of Hamburg's prestigious Freie Akademie der Künste, where Winzentsen's films, drawings, paintings, and objects were exhibited in 2020 under the title "Tanz am Horizont."   

In September 2020, Winzentsen's six-minute film "Völkerwanderung – ein Missverständnis" premiered in Hamburg's Metropolis Cinema, with the aim of reconstructing an event that happened about a century ago and possibly lasted over several years. In June 2023, the opening of "Fake, Figuren und Fiktion. Die bewegte Welt des Franz Winzentsen", a comprehensive exhibition of his work, took place at the Kunsthaus Stade.

Franz Winzentsen and his second wife, educationist Ann-Louise Brette-Winzentsen, reside in Stade.