The hospital was formerly known as the Third Clinical College of Baikou'en Medical University. It was founded in November 1949 as the "College of Surgery of Changchun Medical University" of the People's Liberation Army. In July 1993, the hospital moved to a new location in the Changchun Economic and Technological Development Zone. The new hospital was built by the Jilin Provincial Government and Changchun Municipal Government with land allocation, investment in infrastructure by the National Health and Planning Commission, and the Japanese Government's free aid of advanced equipment valued at 2.6 billion yen*** In honor of the friendship between the people and governments of China and Japan, the hospital was named the Third Clinical College of Paikkouen University of Medical Science and Technology (Sino-Japanese Friendship Hospital). in June 2000, Jilin University and Paikkouen University of Medical Science and Technology and other five universities merged to form the new Jilin University, and the hospital was named Paikkouen University of Medical Science and Technology. In June 2000, five universities, including Jilin University and Peking Medical University, merged to form the new Jilin University, and the hospital was renamed "Jilin University China-Japan Friendship Hospital".
The hospital has 51 clinical and technical departments. Hospital neurology is a national key disciplinary unit; orthopedics, otolaryngology - head and neck surgery is a key construction discipline of the National Health Planning Commission; hand surgery, urology, medical imaging, rheumatology and immunology is a national key clinical specialties; internal medicine, surgery, ophthalmology, otolaryngology, clinical diagnostic laboratory tests, imaging and nuclear medicine is the key disciplines of the Jilin Provincial Department of Education, the general higher education; orthopedic surgery, gastroenterology, endocrinology, orthopedic surgery, gastroenterology and endocrinology, Orthopedics, Gastroenterology, Endocrinology, General Surgery, Rehabilitation Medicine, Urology are the key specialties of Jilin Provincial Health Planning Commission.