Human Immunodeficiency Virus (HIV) has disproportionately affected various population groups, including adolescents living with HIV (ALHIV). In many contexts, ALHIV have been reported to experience mental health issues following their HIV diagnosis. However, there is a limited understanding of the mental health issues faced by ALHIV in Indonesia and the various contributing factors globally. This study aimed to explore the mental health challenges and their contributing factors among Indonesian ALHIV. A qualitative design employing one-on-one in-depth interviews was used to collect data from ALHIV ( = 20) in Yogyakarta, Indonesia. Participants were recruited using the snowball sampling technique, beginning with the dissemination of study information sheets through a healthcare facility that provides HIV care services and via a WhatsApp group for adolescents living with HIV. The data were thematically analyzed, guided by a qualitative data analysis framework. The findings showed that ALHIV experienced a variety of mental health challenges upon learning of their HIV-positive status. Their mental health was also influenced by a range of family-related factors, stigma, and discrimination, which were also facilitated by their specific situations and settings, including living in a shared house with parents and siblings and school setting where they met and interacted with different peer groups on a daily basis. Family-related factors, including broken homes, family conflicts, lack of family support, and being orphans, negatively impacted their mental health. The awareness of perceived and anticipated stigma, and the experience of enacted stigma or discrimination, also contributed to the mental health challenges they faced. The findings indicate a pressing need for tailored and targeted HIV intervention programs and activities that support their mental health, reduce stigma, and promote HIV status disclosure in safe ways for ALHIV both within the study setting and beyond.