National Taiwan University Children’s Hospital (NTUCH) is affiliated with National Taiwan University Hospital (NTUH). The overall operation and business strategy of NTUCH is assisted by various units, personnel, and committees serving in the Children's Medical Building to plan, guide, supervise, and review, in order to cultivate top-notch pediatric medical research and professional talents and improve the quality of pediatric medical care in Taiwan and international competitiveness. In the future, additional committees and functional units will be established depending on the business needs of education, research, and medical care.

After the establishment of NTUCH, due to related regulations of the total staff quota, the required personnel will be allocated from the existing staff of the main hospital without increasing the staff quota. Moreover, due to the current financial difficulties and limited resources of the government, the relevant administrative departments and medical resource units will be shared with NTUH to avoid a decrease in the quality of medical care caused by scattered human and material resources in the short term.

NTUCH has one director who supervises the operation of the Children's Hospital. Each medical department has a department head who is responsible for the medical business of each department. In addition, there are medical support, administrative, and research units jointly responsible for the business of NTUCH, making it a functional organization. The organization of NTUCH is as follows: