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Siddiqui went to the National School of Drama, New Delhi. After graduating from NSD in 1996, he moved to Mumbai. 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. In 2009, he appeared in a cameo role in the song "Emotional Atyachar" in the movie Dev D in his role of Rangila, along with his duet partner Rasila (known together as Patna ke Presley). In the same year, he appeared in New York (2009). However, it was his role of a journalist in Anusha Rizvi's Peepli Live (2010), that first got him wide recognition as an actor. In 2012, he appeared in Prashant Bhargava's Patang : The Kite (2012) which premiered at the Berlin International Film Festival and the Tribeca Film Festival, for which Siddiqui's performance was praised by film critic Roger Ebert, a role which "transformed his acting style". The film was subsequently released in the U.S. and Canada, and garnered much attention with rave reviews from the New York Times. He then appeared in Kahaani (2012), in which he played the archetypal short-tempered intelligence officer Khan. Anurag Kashyap's gangster epic Gangs of Wasseypur followed, which furthered his fame. He played his first primary role as Sonu Duggal in Ashim Ahluwalia's Miss Lovely, which premiered at the 2012 Cannes Film Festival, a role Siddiqui describes as his "most real performance so far." Siddiqui then followed this up with the sequel to Gangs of Wasseypur. In 2013, he played the lead role in the horror flick Aatma. He appeared in Aamir Khan's 2012 release Talash. In 2014, he played lead antagonist Shiv Gajra, in the blockbuster Kick. In 2015, Siddiqui's films Bajrangi Bhaijaan and Manjhi - The Mountain Man were released, and he was praised for his roles. Siddiqui appeared in a film based in Gujarat, titled Haraamkhor. For his performance in Haramkhor, he was awarded "Best Actor" at the New York Indian Film Festival. Siddiqui received the Special Jury Award at the 2012 National Film Awards. and the Filmfare Award for Best Supporting Actor in 2013. Siddiqui portrayed Balasaheb Thackeray in the biopic Thackeray.