After the independence of Pakistan and India in 1947, Nawab M. Ismail Khan remained a member of the Legislative Assembly of India. He accepted in 1947 to become the Vice-Chancellor of Aligarh Muslim University for the second time, only to confront the challenge facing the very existence of the Muslim character of the Aligarh Muslim University -– it was Nawab M. Ismail Khan who invited Jawaharlal Nehru and Mrs. Sarojini Naidu to the convocations of the University whereby giving it the official recognition of the Indian Government. The moment he sensed that the University might suffer on account of his presence, he resigned immediately and returned to Meerut in 1948. His association with the Aligarh University was deeply rooted due to his father, Nawab M. Ishak Khan, who had served the institution with passion and devotion as its Trustee and Secretary when it was the M.A.O. College. Nawab M. Ismail Khan also served the University for many years as its Trustee.