He also worked as an associate professor at the Universiti Brunei Darussalam from 1993 to 1999, after which he returned to Pakistan. Mushtaq is a tenured professor at Quaid-i-Azam University, and a former syndicate member, Quaid-i-Azam University, Islamabad. He is also an honorary full professor at the Mathematics Division, Institute for Basic Research, Florida, US. He served as vice chancellor of The Islamia University of Bahawalpur from 19 December 2014 to December 2018. He has parametrised actions of the modular group on projective lines over Galois fields. This method has proven to be so effective and rewarding, that its wide uses can be seen in Combinatorial Group Theory, Algebraic Number Theory, and Theory of Group Graphs. His graphical technique helped to solve George Abram Miller's problem (1901) on alternating groups as homomorphic images of the modular group  He has also invented a new algebraic structure known as Locally Associative LA-semigroup, and has done some fundamental research on LA-semigroups producing some significant results in this theory. Consequently, a number of useful mathematical results have emerged which otherwise were applicable under restricted conditions only. Mushtaq has collaborated in research with the late Graham HigmanFRS (Oxford) and the late Gian-Carlo Rota (MIT). He has been an invited speaker at Oxford University, MSRI Berkeley, Harvard University, Massachusetts Institute of Technology and Southampton University; and an invited speaker at several international conferences. He has supervised, as a sole supervisor, the highest number of M.Phil. and PhD students in Pure Mathematics in Pakistan (see the Mathematics Genealogy Project). As a result, he has established a research group in Pakistan, the largest of its kind, which is producing high level original research in mathematics. Mushtaq has over a hundred research papers to his credit. He has written and edited several books, some of which are, Mathematics: The Islamic Legacy (which received a prize from the National Book Council of Pakistan), published by UNESCO and other international publishers; A Course in Group Theory, and Discrete Lectures in Mathematics. He has also written books on topics other than mathematics. They are, Focus on Pakistan, and Pakistan: An Introduction. He was also an invited writer for the monumental book, comprising six volumes, entitled the History of Civilizations of Central Asia, published by UNESCO (translated into several foreign languages). He is also known for his analytical writings and research articles on history, mathematics, science, education, and philosophy.