Muratović began teaching as an assistant professor at the Faculty of Mechanical Engineering of the University of Sarajevo in 1974. In 1982, he was promoted to lecturer at Faculty of Electrical Engineering, University of Sarajevo and later professor in 1988 in Theory of Systems and Analyses of Information Systems where he lectured until he was elected rector. He was, at the same time, professor in Management and Organization at the Economic Faculty Sarajevo where he founded the Department of M&O and was its manager (1989–2006). As rector of the University of Sarajevo, Muratović reformed the system of high education and introduced the Bologna Process of Higher Education.
He was an author of four and co-author of six books and over 120 papers in the field of strategy, restructuring, organization structures, change, crisis management and negotiations.
Parallel with his academic career, Muratović was also active in business companies transferring his knowledge from research and university to practical projects and management. After finishing his studies in mechanical engineering, he worked in Fabrika motora Sarajevo (largely known as FAMOS) from 1964 to 1973, first as a designer in R&D department and then as a manager of production planning and the manager of strategic planning, finances and information systems. He then joined the United Bus Company of Lusaka, Zambia during the period of 1973–1977 as a regional manager, where he established state passenger transportation. After that assignment, Muratović worked for ten years as a consultant in Institute for Economic and Organization Sarajevo from 1977 until 1987. During that ten-year period, he managed development and construction of large military industry complexes in Iraq.
During the late 1980s and early 1990s, Muratović managed the Institute for Research and Development of UPI, one of the ten biggest companies in the former Yugoslavia. In 1989, he established his own consulting company, BHM, which operated very successfully until the beginning of the war. Muratović was the chairman of the Bosnia version of Deloitte from 2004 to 2008, and then a consultant for Management consulting projects.
Muratović began his political career in the beginning of the Bosnian War. In June 1992, he took position of minister in the first wartime government of the Republic of Bosnia and Herzegovina. He served in different ministerial positions in all six war governments, the longest period as a minister without portfolio and president of State Committee for Cooperation with UNPROFOR (United Nations Protection Force) and other international organizations. He was known as a very successful negotiator. Muratović negotiated also, through all of the war, with enemies (other two warring sides). In memoirist books written by representatives of international organizations, Muratović is described as a tough and rational negotiator. After the Dayton Agreement had been signed, in which signatory ceremony he participated, he became the last Prime Minister of the Republic of Bosnia and Herzegovina on 30 January 1996, serving until 3 January 1997.
During his period as Prime Minister, Muratović created the first plan for post-war reconstruction, together with World Bank expert teams, completed negotiations with Paris and London Clubs and other international financial institutions. He also organised donor conferences held with the support of the High Representative of the UN and EU in which US5.1 billion was collected for the post-war recovery. Muratović was also governor of Bosnia and Herzegovina for the World Bank from 1996 to 1998. He acted as a leader of two election campaigns for the Party of Democratic Action (SDA) in 1996 and in 2002. In both he obtained the best results.
After the first post-war elections, Muratović became the first Minister of Foreign Trade and Economic Relations on 3 January 1997, but resigned two years later after getting appointed as Bosnia and Herzegovina Ambassador to Croatia on 4 February 1999.[citation needed] In 2002, he left the ambassador role and became the Vice President of the Parliamentary Assembly of the Council of Europe. Muratović resigned from that position in 2004, taking the new position of rector at the University of Sarajevo.
Muratović lived in Sarajevo, Bosnia and Herzegovina up to his death, where he was married to Mulija Čabaravdić and had two sons: Amir, film director and architect and Faruk, management consultant.