Films directed by him include Chander Pahar (2013), Meghe Dhaka Tara (2013), Amazon Obhijaan (2017) Cockpit (2017).

His next venture was Meghe Dhaka Tara, inspired by the life and works of Bengali filmmaker, Ritwik Ghatak.

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.

[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.