Allen was appointed a medical missionary and sent to China by the Board of Foreign Missions of the
Northern Presbyterian Church and arrived in Shanghai on October 11, 1883. After a while, he decided to serve in Korea, which had just opened its doors to the western world. After obtaining the mission board's permission, he went to Korea on September 20, 1884, to explore. As government law prohibited foreign religion at the time, he was appointed medical officer of the United States Legation to Korea in Seoul, thus hiding his true identity. He went back to Shanghai to bring back his wife Francis "Fannie" and their son, Harry to Korea on October 26. On December 4, 1884, the
Gapsin Coup, a coup d'état staged with the help of the Japanese army by a handful of elite progressive officials, took place. The progressive government collapsed in 3 days as the Chinese army entered Seoul and defeated the Japanese army. This event started with the assassination attempt on the life of the queen's nephew, , who was hosting a banquet to celebrate the opening of the nation's first postal office with dignitaries including foreign diplomats and he was inflicted with 7 severe sword wounds. Dr. Allen was summoned and treated Min's near-mortal wounds, applying western medical methods against the objection of 14 of the court's medicine men. It is noted that wounds soon became infected and Dr. Allen treated the infected wounds with "baked mud" to absorb pus and wash away with water and it took 3 months before Dr. Allen's treatment on him was completed. Upon hearing the widespread rumor that a foreigner with bushy red beard revived a dead prince, many people flocked to his house. He submitted to the Foreign Ministry "A proposal of founding a hospital for the government of His Majesty in Seoul Corea" with an introductory letter by J. C. Foulk,
chargé d'affaires of the U.S. Legation.
Gojong granted his proposal readily and a western hospital named
Gwanghyewon () was opened in a traditional Korean estate on April 10, 1885. The name quickly was changed to
Chejungwon (). The hospital had 5 separate in-patient rooms, eye treatment room for extraction of cataracts, vaccination room for smallpox, etc. A year later, Dr. Allen, John William Heron and
Horace Underwood opened the Medical and Scientific School of the Royal Corean Hospital and admitted 16 medical students. The Severance Hospital and Medical school on June 5, 1962, moved to a new location in Sinchon after building a huge medical complex which included the Eighth U.S. Army Memorial Chest Hospital as an integral part and a separate unit ($400,000 worth of building material and $70,000 for medical equipment as American Forces Aids to Korea Program 1955). This institution now is called Yonsei Health System, part of Yonsei University after union with Yonsei University on Jan 5, 1957. Allen's post Chejungwon activities related to Korea are; King Gojong of Korea asked Allen to help open the Korean Legation in the United States of America and Allen led a 12-man delegation to Washington, D.C. in November 1887 and established the Korean Legation in January 1888 when Minister Park J. Y presented appointment letter to President Cleveland. Allen helped operate the Korean Legation and carried out diplomatic activities (his position was "foreign secretary" "참찬관" ). Upon his return from North America he started working in July 1890 as Secretary at the United States Legation in Seoul and left 15 years later in June 1905 as the Envoy Extraordinaire and the Minister Plenipotential before his successor Morgan closed the United States legation in November 1905. == Death and legacy ==