When the Southern University of Bangladesh was established in Chittagong in 2002, he was appointed its founding VC. He served as the first Director General of the Islamic Foundation Bangladesh. In 1974, he was promoted to the post of Professor in the same department. He established the Department of History and Culture of Islam at Chittagong University in 1973 and joined the department as its founding chairman. After the independence of Bangladesh in 1971, he returned to the country and joined the history department of Chittagong University in 1972 as an associate professor. He then became an associate professor at the Islamic Research Institute in Islamabad in 1966. Khan was appointed a lecturer in the history of Islam at Karachi University in 1961. While studying at McGill University in Canada, he met Wilfred Cantwell Smith, a well-known Western orientalist and the founder of the Institute of Islamic Studies, and extended his knowledge of Islam. He completed a seminar in political science at the Institute of South Asian Studies at the University of California, Berkeley, after receiving a postgraduate fellowship.
He received his PhD from the University of Dhaka for his work on Social History of Bengal under the supervision of Ahmad Hassan Dani, a renowned archaeologist of the Indian subcontinent. He later went on to study at McGill University in Canada with a Fulbright Scholarship and earned a master's degree in Islamic history.
He then enrolled in the Department of Islamic Studies at the University of Dhaka and obtianed his bachelor's and master's degrees in 19 respectively. He passed madrasa in 1945 and completed higher secondary education in 1948. Muinuddin Ahmad Khan was born on April 18, 1926, in the village of Chunti in Lohagara upazila of Chittagong.