Siddiqui made his Bollywood debut in the year 1999, with a small role in the Aamir Khan starrer Sarfarosh. He then appeared in Ram Gopal Varma's Shool (1999), Jungle (2000); and Rajkumar Hirani's Munnabhai MBBS (2003). After moving to Mumbai he tried to get work in television serials, but did not achieve much success. He did a short film, The Bypass in 2003, where he appeared with Irrfan Khan. Beyond that between 2002–05, he was largely out of work, and lived in a flat that he shared with four other people, and survived by conducting occasional acting workshops. In 2004, which was one of the worst years of his struggle, he couldn't pay any rent. He asked an NSD senior if he could stay with him. The senior allowed him to share his apartment in Goregaon if he was willing to cook meals for him.