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Medical and public health administration in Hualien could be traced back to Hualien Harbor Office set by Emperor Xuantong of Qing Dynasty in 1909. The Health Department under Hualien Harbor Office was the first public health agency.

Four facilities at that time (Hualien Harbor Hospital established in 1910, Qilai Hospital established in 1913, Hualien Harbor Clinic under Hualien Railway Administration Office, and Pushige Clinic) provided basic medical service and formed the foundation of modern public hospital system.

The Hualien County Government established in 1946 reformed previous Health Department to Health Subsection under Civil Affairs Section (1946) and under Hualien County Health Hospital later (1947).

Health Subsection under Hualien County Health Hospital had four components: general affairs, medical administration, health care and epidemic disease control (with subordinate units: outpatient department, contagious disease department and pathologic examination lab). As a tuberculosis-endemic area, the Hualien County Tuberculosis Control Agency was set up in 1956 accordingly.

In 1961, the Hualien County Government reformed the Health Subsection again into Hualien County Health Bureau as today. Three new offices were established as accounting office, personnel office and civil service ethics office.
Subordinate Chronic Disease Control Center and local public health center in 13 townships were also settled.

Hualien County Health Bureau is now located in Hualien Sanitation and Health District since 1998, accompanied by Center of Disease Control-East District and Hualien Public Health Center.

There were several office locations previously:
Our first office was at Hualien County Health Center where was supported by public health and medical project. In 1963, the Health Building was built by the Health Department of the Executive Yuan with financial support from the US. In the Health Building, we shared floors with Provincial Hualien Hospital, and combined medical administration with public health service closely. Hualien Health Bureau subsequently moved to another office from 1973 to 1998, for Provincial Hualien Hospital's and our service expansion. The Hualien County Government donated the land and building budget of 1.5 million NTD.