Abstract Background Lesbian, gay, bisexual men, and transgender persons (LGBT) in Kenya and Rwanda have a hard time accessing healthcare, in particular sexual health screening. We used a social norms and values framework to examine determinants of access to healthcare, with specific attention to sexual healthcare. Methods We draw on cross-sectional mixed methods research in Kenya and Rwanda that examined the lived experiences of sexual and gender minorities in access to health services. A cross-sectional quantitative survey in Rwanda (n = 499) and Kenya (n = 1,550) was conducted with LGBT people. We conducted key informant interviews (n = 81), in-depth interviews (n = 48), digital storytelling (n = 3), and focus group discussions (n = 30). We used a mixed-methods thematic and content analysis to integrate quantitative and qualitative findings. Findings Accessibility and quality of care were the main barriers to healthcare services. The results indicate widespread discrimination and stigma toward LGBT people in service provision. Approximately half of the survey participants, 47%, reported challenges accessing health services, and 25% indicated they experienced discrimination in healthcare. Qualitative results link low quality of care to stigma and discrimination. “Mostly at the hospitals, there are times people take too much time discussing who we are instead of giving us the treatment we seek, and send us to mental health to first deal with our sexuality issues since they think it is a ‘sickness.’” (Focus group, Muhanga, Rwanda). Our study highlights challenges in navigating sexual healthcare in government, faith-based, and donor-funded health facilities. Conclusions Access to healthcare services, particularly sexual health screening and prevention, is a growing issue for LGBT people in Kenya and Rwanda. Stigma acts as a significant barrier to high-quality healthcare. Sensitivity training and educational opportunities for healthcare professionals are urgently needed to address stigma.