The Department of Economics accommodates two research centers that are staffed by scholars from and outside Boğaziçi University: Center for Economic Design and Center for Economics and Econometrics. In addition, the Department of Economics is one of the founders and mentors of the Center for European Studies.

Center for Economic Design (CED) was established in 1994 in order to bring together various research activities in the field of economic theory that had been taking place at Boğaziçi University and in Turkey. The strategic goal of CED has been to become a leading center of excellence in economic design, which applies the accumulated traditions and wealth of knowledge in normative and positive economics and game theory in the creative tasks of designing and implementing diverse legal-economic instruments. These include constitutions and other assignment of rights, voting and other choice aggregation procedures, mechanisms for resource allocation and regulatory mechanisms, tax and incentive schemes, contract forms, markets, auctions, as well as organizational forms, such as partnerships, together with supporting membership and other property rights, and information systems. Towards this end, CED supports theoretical and applied work in the field of economic design; communicates and collaborate with local, European and other international educational and research institutions in this field to support graduate education and to carry on joint projects; encourages and facilitate the dissemination of knowledge relevant to economic design via publications in this field; and organizes and participates with its members in workshops, seminars and conferences. CED is an institutional member of the Association of Southern European Economic Theorists (ASSET).

Center for Economics and Econometrics (CEE) was founded in 1994 to bring together applied economists, solid in modern theory and analysis, and enable them conduct policy oriented research. The research associates have hands on experience with empirical issues and large data bases, including survey data. Competences of CEE include international economics and international finance, macroeconomics (macro-econometrics, stabilization policy), banking, labor market and growth (employment, internal and international migration), trade and applied industrial organization (micro-econometrics, panel data techniques, impact of EU on Turkish economy).

Center for European Studies (CES) was established in 1991, with the objective of conducting interdisciplinary research, emphasizing the cultural dimension of Turco-European relations in a comparative framework. In 2000, the University decided to broaden the scope of the studies conducted at the Center to cover all major areas in social sciences. CES aims at providing an academic and intellectual forum on multiple aspects of the European integration process with an emphasis on the accession of Turkey and other candidates. CES promotes academic research and functions as a focal point for debate on EU-Turkey relations as a think-tank comprising academics and practitioners from the public and private sectors and the NGOs.