Marcel Jean came to the NFB in 1998, serving as special producer for Collections for a year. In that capacity, he packaged the complete works of Pierre Perrault on video and DVD as part of the Collection Mémoire series. He also created several compilation series for television.

In 1999, he was named a producer in the Animation and Youth Studio, replacing Pierre Hébert. He oversaw the completion of several projects released in 2000, including Martine Chartrand's Black Soul/Âme Noire (winner of the 2002 Jutra Award for best animated film), Claude Cloutier's From the Big Bang to Tuesday Morning, and Abi Feijo's Clandestin/Stowaway (co-produced with Portugal's Filmografo). More recent productions include La Pirouette/Pirouette (directed by Tali, 2002), Parfum de lumière/Fragrant Light (Serge Clément, 2002), Nuit d'orage/Stormy Night (Michèle Lemieux, 2003) and Accordéon/Accordion (Michèle Cournoyer, 2004).

Under his leadership, the Animation and Youth Studio emphasized auteur animation, highlighting a wide range of approaches and ongoing experimentation with the medium. Jean has also strongly committed the studio to encouraging production from outside of Montreal, allowing young animators from less populous regions to direct their first professional films. Patrick Bouchard, from Saguenay, won best animated film at the 2003 Jutra Awards for Les Ramoneurs cérébraux/The Brainwashers (2002). Meanwhile, Quebec City's Kiwistiti Collective directed Rumeurs/Rumours (2003) and Jean Detheux, a Franco-Ontarian visual artist, has moved to film with Liaisons and Rupture, both released in 2005.

The Animation and Youth Studio has had a longstanding interest in international co-productions. Jean has built on the work of his predecessors, inking an agreement with France's Folimage studio that creates an animation filmmaker in residence program. Through the partnership with Folimage, Jean has already produced Zodiac (directed by Oerd Van Cuijlenborg, 2001), Francois Le Vaillant/Francesc lo Valent (Carlès Porta Garcia, 2001) and Circuit marine (Isabelle Favez, 2003). Ruzz et Ben/Ruzz and Ben, directed by Philippe Julien and co-produced by JPL Films, is another partnership with France.

The studio is also deepening links with Scandinavia. The Animation and Youth Studio co-produced two films by Pjotr Sapegin: Aria (2001) and the multi-award-winning A travers mes grosses lunettes/Through My Thick Glasses (2004) with the Norwegian company Pravda. Danish production house Zentropa is another Scandinavian partner, co-producing Leif Marcussen's Angeli, released in 2002.

Meanwhile, Jean and legendary animator Georges Schwizgebel worked together on 2004's L'homme sans ombre, co-produced with the Swiss studio GDS. It went on to win numerous international awards. He also co-produced Jeu, another Schwizgebel film, along with Florence Miailhe's Conte de quartier and Regina Pessoa's Histoire tragique avec une fin heureuse.

Jean was deeply involved in the worlds of film and publishing before coming to the NFB. He served as film critic for the daily Le Devoir and the magazine 24 Images, co-wrote Le Dictionnaire du cinéma québécois with Michel Coulombe, and was collections director at the publishing house Les 400 coups.

He has also directed five films of his own, including Vacheries (1990), État critique (1991) and Écrire pour penser (1999). He is well known for his interest in animation, having written two books on the topic: Le Langage des lignes (1995) and Pierre Hébert, l'homme animé (1996). He also held the position of animation curator at the Cinémathèque québécoise from 1996 to 1998 and has taught animation history and aesthetics at Université de Montréal for 20 years.

In June 2005, Jean resigned as head of the NFB's Animation and Youth Studio.