SHH was previously called Peking University School of Foundational Education. SHH has a long history of academic tradition, with the first teaching and research divisions for the History of Medicine, Medical Psychology and Medical Ethics in China being established here.

When Beijing Medical University (the predecessor of PKUHSC) was founded in 1912, teachers in German, Chinese, Ethics and Gymnastics were employed. In 1929，subjects like Chinese，German，Mathematics and Physical Education were listed as  compulsory courses, while English, Japanese, History of Medicine, Physician Ethics and Sociology were included in the elective courses.

Since 1940s, with teaching and research sections related to humanities being built up, the health humanities discipline construction began to take shape. The Division on History of Medicine was set up in 1946 (later renamed as Teaching and Research Section on History of Medicine in 1952), which is the first department of the history of medicine in China. The first director was Professor Li Tao, who was also one of the initiators and presidents for the Chinese Society of Medical History of Chinese Medical Association, and acted as the chief editor of Chinese Journal of Medical History. From the year 1962, Beijing Medical University has enhanced the teaching on foreign language and political theories, and set up medical statistic courses for postgraduate students.

After the Third Plenary Session of the 11th Central Committee of CPC, all disciplines had further development. In 1979, the teaching and research section on Medical Psychology was set up in response to the shift of medical models. In 1981, the teaching and research section on Moral Education was built up. In 1983, the Marxism-Leninism teaching and research section made exploratory reform on the course of the History of Chinese Communist Party, adding the content of Chinese modern history and renaming the course to the History of Chinese Revolution. This reform received high recognition from the State Education Commission of the PRC, who recommended all other universities to conduct similar reforms. In 1985, Beijing Medical University decided to strengthen the development of courses in social sciences and set up the Department of Social Sciences and Humanities in March, which comprises teaching and research sections in History of Chinese Revolution, Political Economics, Philosophy, Ideological and Political education, Medical Psychology and History of Medicine. The teaching and research section on Medical Ethics was set up in 1988. In 1990, the university had revised the postgraduate curriculum, adding Statistics and Computer Sciences into the foundational course list.

After Beijing Medical University incorporated into Peking University in 2002, and renamed to Peking University Health Science Center (PKUHSC), to enhance medical students’ foundational and liberal arts education, the School of Foundational Education was founded in July 2002 by combining the former divisions related to basic literacy education, including Division of Social Sciences and Humanities at Beijing Medical University, Division of Foreign Language Education, Division of Physical Education, and the teaching and research sections of Mathematics, Physics and Computer Science at the School of Basic Medical Sciences. To respond to the modern transformation of models on medicine and new initiatives on health care systems, based on the infrastructure of the School of Foundational Education, the Institute for Medical Humanities was established in April 2008, which was formally renamed as School of Health Humanities on November 2018.