Background <p>People who identify as transgender have a gender identity or expression that differs from the sex they were assigned at birth. Because of this, transgender people may encounter widespread stigma, discrimination, and violence, including in medical facilities. Understanding how these phenomena manifest during healthcare interactions is crucial for enhancing health equity for transgender individuals. Therefore, this study explored the experiences of transgender-related stigma and violence among transgender individuals in Uganda.</p> Methods <p>The study used a community-based qualitative participatory approach, with transgender women actively co-generating the data. Six focus groups were held with 33 transgender women in southwestern and central Uganda. Data were thematically analysed using OpenCode software.</p> Results <p>Four key themes emerged for the lived experiences of violence and abuse among transgender women in Uganda. These included: (i) Institutionalized physical violence and violation of bodily autonomy, (ii) Religious impositions and moral policing, (iii) Dehumanising treatment and objectification and (iv) Systemic discrimination and denial of care.</p> Conclusions <p>In conclusion, this study highlights the pervasive violence, abuse, sexual assault and discrimination reported by transgender women in healthcare settings in Uganda. These experiences not only compromise access to quality healthcare but also perpetuate stigma and exacerbate health disparities. Addressing these issues requires comprehensive, trauma-informed care, alongside structural reforms and training for healthcare providers. Ensuring respectful, affirming, and inclusive healthcare environments is essential to safeguarding the rights and well-being of transgender individuals. Additionally, more studies should evaluate the effectiveness of interventions like healthcare provider training and addressing social determinants of health to determine the most impactful strategies for reducing violence.</p>