Mukherjee's career began with All India Radio. He started acting in Bengali films in 1950. The first film directed by him was "Maa" (1956) in Bengali language. Mukherjee directed three more films till 1960. Assamese film "Puberun", directed by Mukerjee was released in 1959. The film was screened at the 1960 Berlin Film Festival. He also wrote the script for the film. From 1972 to 1984, Mukherjee made at least five Oriya films. One of these is "Ratnakar" (1982), which was the first film of Odia actor and director Prashant Nanda. In 1972 Mukherjee directed his first Hindi-language film "Shayar-e-Kashmir Mahjoor", which was a biopic on Ghulam Ahmad (1885-1952), the famous national poet of Kashmir and produced by Government of Jammu and Kashmir. Balraj Sahni played the title role. After that Mukherjee directed two more Hindi films before coming back to Bengali films.