Eberhard Junkersdorf started his career in the movie business at the beginning of the 1960s as a unit manager at Rialto Film Preben Philipsen. In the mid-1960s, he came into contact with French and US production companies and directors, for instance while shooting the French-German co-production "Winnetou II" ("Last of the Renegades", 1964). From 1967 on, Junkersdorf worked at Independent Film for several comedies directed by Kurt Hoffmann.

In 1970, Junkersdorf started another collaboration that heavily influenced his further career and produced "Der plötzliche Reichtum der armen Leute von Kombach" ("The Sudden Wealth of the Poor People of Kombach") for Peter Fleischmann's and Volker Schlöndorff's production company Hallelujah-Film. Junkersdorf was also in charge of Schlöndorff's following films and served as a co-producer for "Lacombe Lucien", directed by Louis Malle.

In 1973, Junkersdorf set up Bioskop Film GmbH together with Volker Schlöndorf and Reinhard Hauff. Productions supervised by Junkersdorf include Achternbusch's "Das Andechser Gefühl", von Trotta's "Die bleierne Zeit" ("Marianne and Juliane", 1981) and "Rosa Luxemburg" (1986), as well as Hauff's "Messer im Kopf" ("Knife in the Head", 1978) and "Stammheim" (1985), that won the Golden Bear at the Berlin international film festival. Bioskop Film repeatedly served as co-producer for the films Volker Schlöndorff made in France and in the USA. These productions were highlighted by Academy Award nomination for Schlöndorff's film "Die Blechtrommel" ("The Tin Drum", 1979), an adaptation of the novel by Günter Grass.

In the mid-1990s, Junkersdorf turned to animation films and set up the animation film studio Munich Animation in 1995. In 1997, he debuted as a director with "Die furchtlosen Vier" ("The Fearless Four"). The film won the Bavarian film award. Junkersdorf then also directed the German-Belgian co-production of the animated film version of "Till Eulenspiegel" ("Jester Till") that was nominated for an Academy Award for animation films in 2003.

In 2002, Junkersdorf set up Neue Bioskop Germany (NGB1) that produced Oskar Roehler's Berlinale entry "Der alte Affe Angst" ("Angst", 2003), among others.

Junkersdorf serves as honorary chairman of Arbeitsgemeinschaft Neuer Deutscher Spielfilmproduzenten and as chairman of the supervising board and of the presidium of Filmförderungsanstalt (FFA) Berlin, whose honorary president he is today. From February 2008 to March 2015, he was chairman of the board of trustees of the Friedrich-Wilhelm-Murnau-Stiftung in Wiesbaden.

In 2001, Eberhard Junkersdorf was awarded with the Federal Cross of Merit, First Class, and in 2004 he received the Bavarian Order of Merit.