The University was founded in 1885, when modernization of Korea was about to begin. On April 10 of that year, Dr. Allen, the American missionary who was also serving as a physician to King Kojong, was granted royal permission to establish in downtown Seoul a modern Western-style hospital named Kwanghaewon (later renamed Chaejung-won), which was to grow to become today's Severance Hospital and thus the start of Yonsei University.

In 1947, the hospital was formally authorized as Severance Union Medical College, and in January, 1957, the College and Chosun Christian University, another institution eatablished in 1915 by american missionaries, were merged into Yonsei University.