Gender and race issues have caused rapid cultural and societal changes to affect the healthcare of indigenous women, which involves complicated, cultural meanings. The present paper begins by outlining the gender perspective and then elaborates on the present gender mainstreaming and status of indigenous women’s healthcare in Taiwan. Furthermore, this paper identifies the current difficulties experienced by Taiwanese indigenous women, including those related to the lack of adequate healthcare data and gender analyses on indigenous women and the lack of regular research on healthcare strategies for indigenous women. Therefore, the present paper proposes to establish health policy references that are gender and race sensitive. The health policy not only addresses racial and gender concerns regarding healthcare information but also focuses on the analysis of indigenous healthcare information. Indigenous women’s health concerns are discussed here within the framework of healthcare policy through the perspective of gender mainstreaming. Additionally, we will analyze and evaluate the effects of gender in order to establish inspection and management processes that integrate the concept of gender into policy development and implementation, thus promoting relevant health policies. During the processes of planning, implementing, and evaluating healthcare policies, women should unite to contribute toward indigenous women’s health policies and gender mainstreaming.