His father Sir Ashuthosh Mookerjee was a widely known advocate in Bengal. He was a graduate of Calcutta University. He became a fellow of the Senate in 1923. He enrolled as an advocate in Calcutta High Court in 1924 after his father's death. Subsequently he left for England in 1926 to study in Lincoln's Inn and became a barrister in 1927. At the age of 33, he became the youngest Vice-Chancellor of the Calcutta University and held the office till 1938. He was elected as member of the Legislative Council of Bengal as a Congress candidate representing Calcutta University but resigned next year when Congress decided to boycott the legislature. Subsequently, he contested the election as an independent and got elected.
He emerged as a spokesman for Hindus and shortly joined Hindu Mahasabha and in 1944, he became the President. After the assassination of Mahatma Gandhi, he wanted the Hindu Mahasabha not to be restricted to Hindus alone or work as apolitical body for the service of masses and broke away from it on this issue on November 23, 1948.
Pandit Nehru inducted him in the Interim Central Government as a Minister for Industry and supply. On issue of Delhi pact with Liaqat Ali Khan, Mookerjee resigned from the Cabinet on April 6, 1950. After consultation with Shri Golwalkar Guruji of RSS Shri Mookerjee founded Bharatiya Jana Sangh on October 21, 1951 at Delhi and he became the first President of it.
In 1952 elections, Bharatiya Jana Sangh won 3 seats in Parliament one of them being that of Shri Mookerjee.