Born in Sušice, Czechoslovakia, Pojar started his career in the late 1940s with his work on The Story of the Bass Cello (1949) based on the story by Anton Chekhov and directed by master Czech puppet animator Jiří Trnka. Pojar served as a puppeteer under his mentor Trnka.
Pojar compiled an extensive body of work as a director and animator in Czechoslovakia, where he made films in both puppet animation to the more common stop motion animation. He worked with the United Nations for the two films Boom and The Big If (with Vaclav Strnad worked as a producer in the latter).
Pojar's work is characterized by strong social commentary, such as in Balablok, where armies of small circle- and square-shaped beings war with each other until they are all wounded into indistinguishable shapes. Often, Pojar's shorts contain little or no spoken dialogue.
In the mid-2000s, Pojar moved back to the Czech film business in order to co-direct the collaborative animated feature film Fimfárum 2 (based on the stories of Jan Werich), which was released in 2006.