His directorial debut, the well acclaimed film Uro Chithi was released in 2011. This film interwove 12 text messages with 12 different characters, combining shades of life spanning across 12 months. His next venture was Meghe Dhaka Tara, inspired by the life and works of Bengali filmmaker, Ritwik Ghatak. The film attempts to portray the period of Ghatak's life when he was admitted into a mental asylum for treatment. Meghe Dhaka Tara was a critically acclaimed film in the Bengali film circuit, and it won the International Film Festival of India Centenary award.
His next film was Chander Pahar (2013), based on a novel by Bibhutibhushan Bandyopadhyay by the same name. Chander Pahar is the second costliest film made in Bengali language and is still the second biggest blockbuster in the history of Bengali cinema.The film received huge critical acclaim. The adventure film was shot in Africa. Then he made the film Khawto, that deals with the love story of an eminent urban author in self imposed asylum near the sea. In 2017, Mukherjee wrote and directed Amazon Obhijaan, (the sequel to Chander Pahar) - that was the costliest Bengali film ever made.[citation needed] Upon release, it was released in 5 languages. The film grossed above 50 crore after being released and is the highest grossing Bengali film to date.[1] Then he made films such as Cockpit - dealing with the life and journey of a pilot, Good Night City based on the conflict between a psychiatrist and a schizophrenic man, Mukhomukhi - a surreal representation of modern-day urban angst and living and Password - a story relating to cybercrime.
As an actor he has performed in a lot of films. Mukherjee is also a playwright, director and the founder member of Kolkata‐based theatre group Shailushik. He is also trained in photography and computer graphics.