President A.P.J. Abdul Kalam will present the award to Sen at the 51st national film awards function Feb 2 in New Delhi.
The award is given by the government of India to acknowledge outstanding contribution in the field of Indian cinema.
Sen, a critically acclaimed filmmaker, was born on May 14, 1923, in Faridpur, now in Bangladesh.
His first feature film was 'Raat Bhore', which was followed by 'Neel Akasher Neechay'. He won fame with 'Bhuvan Shome' in 1969 and the later 'Calcutta 71', but it was 'Kharij' that bagged awards in Cannes, Venice, Berlin and Karlovy Vary.
A member of the National Film Development Corporation, Sen was a member of the Rajya Sabha from 1998 to 2003. He has also received the Padma Bhushan.