Yoon was born in Montreal, Quebec and grew up in Blacksburg, VA. As an undergraduate at Harvard University, he became fascinated by organic chemistry working in the laboratories of leading experts in contemporary asymmetric synthesis. Specifically, Yoon first experienced research in David A. Evans's lab studying stereocontrolled aldol reactions.
After earning his A.B. in chemistry from Harvard in 1996, he proceeded to earn his M.S. under the guidance of Erick M. Carreira, who introduced Yoon to synthesis of complex natural products through applied photochemistry. Yoon was then accepted as Dave MacMillan's first graduate student, initially at UC Berkeley and later at Caltech, where he earned his Ph.D. investigating methods to control the stereochemistry of pericyclic reactions. He returned to Harvard in 2002 as a postdoc to research the use of hydrogen bonding urea catalysts in asymmetric synthesis in the laboratory of Eric Jacobsen.