Malik Zidi was born in Châtenay-Malabry to a Kabyle Algerian father and a Breton mother. He spent his formative years in Saint-Maur-des-Fossés, a suburb of Paris. Zidi abandoned his conventional studies early to concentrate on a career in comedy. Following courses at the Théâtre Véronique Nordey, and the Théâtre de Proposition in Paris, he briefly studied acrobatics and mime at the Théâtre de la Piscine and cinema at the Studio Pygmalion. Zidi made his first film appearance in the 1998 Sébastien Lifshitz-directed Les Corps ouverts.

In 2000, Zidi was chosen by director François Ozon to appear as the troubled, lovelorn, bisexual youth Franz in the Teddy Award-winning film Water Drops on Burning Rocks (French:Gouttes d'eau sur pierres brûlantes). The film was based on the play Tropfen auf heisse Steine by German film director and screenwriter Rainer Werner Fassbinder. The film is a four-part comedy-drama shot entirely on one set and featuring only four actors: Zidi, Bernard Giraudeau, Ludivine Sagnier and American actress Anna Levine. Zidi's role in Water Drops on Burning Rocks garnered him his first of four César Award nominations.