His debut feature, Diamonds of the Night (Barrandov Film Studio), which premiered in 1964, was based on a story by Arnošt Lustig and followed two Jewish boys escaping from a transport during the Holocaust. His second film, A Report on the Party and the Guests (Barrandov Film Studio, 1966), voted Best Film of the Year by Film and Filming Magazine, brought him prohibition from further film work. A complete ban followed in 1968, after he smuggled to the West his footage of Soviet tanks in the streets of Prague.

Jan Němec left Czechoslovakia in 1974 and went to live in France, Germany, UK, Sweden and USA. After the fall of communism in 1989, he returned to the Czech Republic and started to work again. In 2002, he was recognized for this work with the State Award given by president Václav Havel. In 2014, protesting against the current president Milos Zeman's policy, Němec decided to return the decoration.

Upon his death, Jan Němec was working on his new autobiographical comedy The Wolf from Royal Wineyard produced by Masterfilm, where Jiří Mádl plays young Němec.