Although the number of women civil servants has increased over recent years, they, are still under-represent in upper echelons (high leader positions). This phenomenon shows that there is gender disparity in upper echelons. This paper analyses why there is a gender bias in the promotion of civil servants to the upper echelons, and identifies the factors that lead to it. Although public institutions have provided access for women civil servants to develop a career, through a process of job promotions that based on competence or merit, women civil servants still face a glass ceiling in their career achievement. This study is conducted using a qualitative method. Data are based on in dept interviews that are conducted with five women civil servants who occupy positions in the upper echelons, key people from the Local Civil Service Agency, who are associated with the selection and promotion of civil servants in the provincial government of the Special Region Yogyakarta (DIY), and key people from the National Civil Service Agency. This study’s findings show that the regulations and policies concerning promotion to structural positions are based on merit or competence. The process of promotion to high leadership positions conducted by the provincial government of DIY is open. Several barriers for women in achieving the upper positions, such as societal barriers, are not proven in this case. Some organisational factors in this case really prevent women from achieving the higher positions, but other factors do not. Some individual factors also act as barriers. This paper recommends that the managers of local government institutions formulate the regulations that are gender sensitive, especially the regulations regarding promotion and selection. For example, there should be career mentoring and support for women to resolve the work-family conflict in order to achieve progress in their career.