On August 15^th, 1945, Japan surrendered and the Republic of China recovered Taiwan. The central government issued the “Organizational Regulations for the Taiwan Provincial Administrative Executive Office,” on December 11^th of the same year, and established the Taitung County Government on January 12^th, 1946. A total of six Sections were established for Hualien, Taitung, and Pingtung according to the organizational regulations: The Secretary’s Office, the Civil Affairs Section, the Finance Section, the Education Section, the Construction Section, and the Police Affairs Section. Among them, the Civil Affairs Section was in charge of local autonomy, household and personnel registrations, civil organizations, cooperative businesses, social welfare, anti-smoking and drug control, and health administration. Therefore, the department's history starts with its predecessor being the “Taitung Hall Police Hall’s Public Health Department.” The Republic of China then ordered to have it changed to the “Taitung County Civil Affairs Department Health Center” in 1945, and was then subsequently changed to the “Taitung County Health Center” in 1947 as it included the Medical Administration Unit, the Epidemic Prevention Unit, the Health Unit, and the General Affairs Unit. The Health Center was located at Beinan Road, Zhongzheng Village, Taitung Township at the time. The “Outline for the Implementation of Local Autonomy by Counties and Cities in the Taiwan Province” was announced on April 24^th, 1950. In January 1951, the “General Rules for the Organization of Counties (Cities) in Taiwan the Province” was issued and the county administrative organization was adjusted to: the mayors of the County and City Governments with the Civil Affairs Bureaus (Section), the Finance Bureaus (Section), and the Health Centers established under the County and City Governments. The Health Centers were responsible for health administration and technical matters.

According to the “History of Public Health Development in Taiwan (6),” the Provincial Health Department received orders to evacuate to Wufeng Township and established the “Taiwan Provincial Government Health Department Taipei Office” due to business needs and began operating on August 3^rd, 1956. Since then, the Office has gradually expanded its operations while the county and city health centers have maintained their original organizational systems, but their operations are still remained under the command and supervision of the Provincial Health Department. In August 1961, Taiwan Province began to implement local autonomy as local health centers were restructured into health bureaus. The Taipei Yangmingshan Administrative Bureau still established a health center that was under the direct jurisdiction of the local county and city governments. The Provincial Health Department took on a more counselary role, and no longer directly supervised the operations of local health departments as they only offered guidance on health technology. However, the appointment and removal of the health directors must still be approved by the Provincial Health Department in advance. In December 1967, the Taipei City Government was restructured into a municipality directly under the Central Government. The Taipei City Health Department, Yangmingshan Health Center, and Taipei Provincial Hospital (the current Taipei City Hospital Zhongxing Branch) and their affiliated institutions were also reorganized under the Taipei City Government. Therefore, on March 27^th, 1961, the original “General Rules for the Organization of Counties (Cities) in the Taiwan Province” was revised and issued as the “Guidelines for the Organizational Regulations of County (City) Governments in the Taiwan Province.” The administrative organization of the county and city governments were adjusted and the health centers were changed to health departments. After the provincial government approved the new county government organizational regulations on July 2nd, 1961, the Civil Affairs and Construction Sections and the Health Centers were reorganized as Departments. On September 11^th, 1962, the “Taitung County Health Department” established seven units that included Sections 1, 2, 3, and 4, a Health Laboratory, a Chief Accounting Office, and Personnel Management Office. The office was located on Weishen Lane 2, Zhongzheng Road, Taitung Township at the time. The subsequent revisions of the organizational regulations for health departments of counties and cities in the Taiwan Province resulted in an expansion to five sections and a Health Laboratory, a Chief Accounting office, and the Personnel Management Office. There was no separate unit for the Department’s general affairs as designated specialists handled them, the Health Laboratory became the sixth section of the department in 1968.

In November 1982, the new building that served as the office for the department was completed and opened at No. 336 Bo'ai Road, Taitung City, Taitung County. During the amendments to Article 5 of the “Organizational Regulations of Taitung County Government” in 1983: “The government has designated the following bureaus and departments as subsidiary entities in charge of relevant matters. 21. Police Department: in charge of police, security, civil defense, mobilization and household registration affairs. 2. Health Department: in charge of sanitation, health care, environmental cleanliness, and environmental protection. 3. Revenue Service Office: in charge of various tax collection matters in the county, and collect national and provincial taxes on behalf of the county.” A seventh section was added in 1984 that was primarily in charge of food hygiene. The Taitung County Environmental Protection Bureau was established in 1990, environmental sanitation and protection businesses were transferred to them from the Second Section of the Health Department. When Volume 3 of the History of Public Health Development in Taiwan was being compiled in 1995-1997, there were seven sections and three offices with a registered staff of 41 people, and the director at the time was Chen Yiguan.