In a condolence message to his son, Bikas Chandra, the President said Chandra was one of the foremost scholars in the country on modern India.
"For his immense contribution towards the study of Indian history, he was honoured with a Padma Bhushan. He will be missed by his large number of friends, colleagues and students," Mukherjee said.
"I convey my heartfelt condolences to the members of the bereaved family and his countless fans and friends. I pray to the Almighty to give you and your family the strength and courage to bear this irreparable loss," the President said.
Chandra, a left-leaning expert in economic and political history of India, died in Gurgaon yesterday after prolonged illness.
Author of 'In the Name of Democracy: The JP Movement and the Emergency', Chandra had written on wide areas including theory of colonialism, national movement, contemporary history and fights against communalism.