Sir Syed recognized Khan's attachment to the college and in 1897 appointed him trustee. Later that year he was appointed professor of law in the college. After Sir Syed's death in 1898, Khan's involvement with the college deepened. He organized the Sir Syed memorial fund to raise the college to a university.
From 1905 to 1917 Sahibzada actively served the Mohammadan Education Conference as its joint secretary. In 1923 he became its president.
Khan was instrumental in establishing students’ voluntary organization, the Anjuman Al-farz or Duty Society. The duty was a student initiative. Its purpose was to collect funds to enable poor students to come to Aligarh and to promote the interest of the college within the Indian Muslim community and the country as a whole.
Khan was vice-chancellor of the university from 1924 to December 1926. Although he was persuaded to continue for a further term of three years, he declined the offer due to ill health. Most buildings and hostels after Sir Syed's death were constructed under his supervision, which gives the campus its charm.
He died on 18 January 1930 and was buried in the ground of the Ahmadi School for the Blind that he had established in Memory of his father. After his death, the A.M.U. old Boys’ Association decided to construct a Hall of residence in his memory in 1932 and in recognition of his valuable contribution named a Hall as Aftab Hall.[4]