Access to HIV/AIDS-related health services among transgender women living with HIV is still a major public health issue in many developing countries, and Indonesia is not an exception. However, reportedly compared to other settings in the country, transgender women in Yogyakarta have a good access to the HIV-related health services. This study aimed to explore perceptions among transgender women living with HIV, locally known as waria, of factors supportive of their access to the services in Yogyakarta, Indonesia. A qualitative inquiry using in-depth interview method was conducted from December 2017 to February 2018 to collect the data from a selection of waria living with HIV (n = 29) recruited using both purposive and snowball sampling techniques. Data analysis employed a thematic approach which was guided by the framework analysis for qualitative data. The findings indicated several health service system-related determinants supportive of waria’s access to HIV/AIDS-related health services. These included the availability of the services, the simplicity and convenience of accessibility to the services and the comfort felt by the participants while accessing the services. Health professionals’ positive attitudes during healthcare provision, social relationships between waria and health professionals, proximity to healthcare facilities, free access to the services, and information sessions on HIV infection and prevention were also reported to enable participants’ access to the services. These findings call to efforts and strengthening of HIV health service system to support and provide equal access to HIV/AIDS-related services including to all Indonesians living with HIV, but more so for transgender women and other high-risk groups such as sex workers and their clients and men who have sex with men.