During the Japanese colonial era, the Department of Health, Kaohsiung City Government was formerly the Health Section under the Police Board of Kaohsiung City. On October 25, 1945, it became the Health Unit under the Civil Affairs Division of Kaohsiung City Government. On January 1, 1947, the Health Yuan of Kaohsiung City was founded and three offices – Medical Administration, Epidemiology, and Administration - were established. The Health Institution Act led to the birth of four divisions and one office - the divisions of Healthcare, Epidemics, Medicine, Administration, and the Office of Examination. Auditors and Human Resource staff were also part of the expansion.
Further restructuring in September of 1961 changed the Public Health Yuan to the Department of Health, which remained under the municipal government. Besides the addition of a Secretary to the Director-General of the Bureau, it was reformed to six divisions and one office - the divisions of Healthcare, Environmental Health, Medical Administration, Pharmaceutical Administration, Nursing, and Administration, and the Office of Examination. Auditors and Human Resource staff were accounted for separately. In 1963, the personnel staff was organized to incorporate the Personnel Office. On April 1, 1964, the Health Team under the Police Bureau was transferred to the Department of Health and became the Hygiene Team. The Department added a Security Division in 1965. On December 25th, 2010, Kaohsiung County merged with Kaohsiung City to form a single special municipality.