Stigma and discrimination negatively impact the prevention, treatment, and care of HIV. The COVID-19 pandemic increased this complexity and created a cluster of synergistic health contexts, wherein the physiological aspects of HIV and the social and environmental conditions increased the vulnerability in health outcomes for youth living with HIV (YPLHIV) in Kampala, Uganda. We used interpretive phenomenological analysis (IPA) and the syndemics framework to understand the lived experiences of YPLHIV. From December 2020 to May 2021, six qualitative focus groups were held with 31 youth living with HIV to understand the lived experiences of YPLHIV. The guided questions used were audio-recorded, transcribed verbatim, and coded for thematic analysis. Findings highlight the complexity of intersecting stigma of HIV and COVID-19 that have worsened antiretroviral treatment adherence and mental health issues due to lack of access to critical needs such as fears of food insecurity, health-related worries, the fear of perishing due to COVID-19, and human rights concerns related to gender and sexual identity. The study recommends addressing human rights–related concerns in addition to health-related concerns to comprehensively mitigate the syndemics of HIV and COVID-19 for YPLHIV in Uganda.