The Department of Economics was founded in 1987 under the initiative of Prof. Dr. Sübidey Togan, who served as the Department Chair and Dean of the Faculty for over a decade. The department was chaired by Prof. Dr. Erinç Yeldan from 1998 to 2003, by Assoc. Prof. Dr. Fatma Taşkın from 2003 to 2011 and by Assoc. Prof. Dr. Selin Sayek Böke from 2011 to 2014. The current Department Chair is Prof. Dr. Refet Gürkaynak.

In 1989, the Department of Economics established its graduate studies by starting the Master of Arts in Economics program, which was further extended to include a full-fledged Ph.D. program. In 2006 with the joint initiative between the Department of Economics Bilkent University and Tilburg University a Dual Master’s degree program was initiated. The Dual M.A. program allows students to specialize in five alternative areas by studying a year at Bilkent and a year at Tilburg Universities, and writing a thesis in each university to be conferred two Master’s degrees.