He was appointed as the 32nd Foreign Minister of South Korea on February 27, 2003.

He served as Korea's eminent representative to and the co-chair of the East Asia Vision Group II for the ASEAN+3 Summit Meeting from September 2011 to October 2012.

Yoon has published several books and about 70 articles in the field of international political economy, Korea's foreign policy, and inter-Korean relations.

He was the recipient of the Korean Government Scholarship (1981–85), the Best Book Award (by the Korean Association of International Studies) (1996), and the Best Teachers' Award (Seoul National University) (2015).

After completing his military service as a lecturer in International Law at the Republic of Korea Naval Academy, he went on to receive a master's degree (1983) and a Ph.D. at Johns Hopkins University's School of Advanced International Studies (SAIS) in 1987 ("Political Economy of Foreign Investment and Productivity: A Historical Observation and Industry-Specific Case Studies").