Background Men who have sex with men (MSM) and transgender women (TGW) in Rwanda are at higher risk than the general population of being subject to sexual and reproductive health (SRH) disparities pertaining to discrimination and marginalization. There is a significant gap in the literature concerning the experiences of MSM and TGW seeking SRH care, and the challenges that ensue. This study uses an MSM and TGW community-informed survey to analyze the barriers and recommendations to accessing SRH care. Methods A quantitative survey was administered to 134 MSM and TGW members of Hope and Care Organization (local non-government organization) in Rwanda to ascertain the magnitude of barriers and assign weight to the recommendations. Results COVID-19 induced restrictions, societal stigma, perceptions of community/local leaders, fear of disclosure/outing, and violence were found as barriers for both MSM and TGW (p≤ 0.05). Unsupportive policy/legal environment and long waiting times/delays were barriers specifically for the MSM whereas healthcare provider lack of knowledge was specifically for TGW (p≤ 0.05). More than 90% of respondents across both groups recommended unrestricted operation and capacity building of LGBTQI+ organizations, strengthening legal support, peer education & mentorship, mental health support/counsellors, increased community outreach, expansion of care to rural areas, sensitization of local, religious leaders and employers. Further specialized training for healthcare providers and more inclusive and accepting insurance were specific to MSM whereas increased media awareness and sensitization of the general population were specific to TGW. Conclusion This study highlights the unmet SRH needs of TGW and MSM while eliciting community informed recommendations that must drive policy change in Rwanda. The most emphasized recommendations include capacity building, economic support, accessible insurance, sensitization of healthcare providers and increased community outreach. The populations reiterated the need for SRH care to be holistic, highlighting the integral role of mental health care inclusion. Overall, psychosocial safety has been a pervasive theme that needs to be addressed to ensure SRH care delivery.