Between 1964 and 1974 Hüfner worked as a research associate at the Max Planck Institute for Educational Research in Berlin. For the next six years, he served as a professor of economics at Teachers College Berlin. And, from 1980 to 2002 he held an appointment as professor of economics at the Freie Universität Berlin. Over the years, Hüfner has held research appointments at Stanford University, the University of Melbourne, Osaka University, the International Institute for Educational Planning (IIEP) in Paris and the International Institute for Peace in Vienna.

Hüfner has served on many boards and committees. Among others, he was member of the Executive Board of the United Nations Association of Germany, the Executive Committee of the World Federation of United Nations Associations (WFUNA), the Governing Board of the International Institute for Educational Planning (IIEP) and the UN Political Advisory Council of the German Foreign Office.

Since 1982 he serves as a member of the Executive Board of the German Commission for UNESCO, since 2003 as a member of the Conciliation and Good Offices Commission to be responsible for seeking the Settlement of Disputes which may arise between State Parties to the UNESCO Convention against Discrimination in Education, and since 2006 as Senior Research Fellow of the Global Policy Forum, New York.

He is a recipient of the Dag Hammarskjöld Medal of the German UNA. He is also Honorary President of WFUNA, Honorary Member of the UNESCO World Heritage Sites Germany and Honorary President of the Berlin Committee for UNESCO.

Hüfner has authored and edited over 50 books and more than 200 articles. His written work has examined the UN system, UN finance, UN reform and related topics. His book on human rights complaints has appeared in twenty editions in eleven languages. Some important recent books are: Peanuts für die UNO- Das deutsche Finanzengagement seit 1960 (2008), UNESCO und Menschenrechte (2008), Die Finanzierung des UN-Systems (2nd edition, 2006), and - together with Jens Martens - UNO-Reform zwischen Utopie und Realität (2000).