In sub-Saharan Africa (SSA), men who have sex with men (MSM) often have female sexual partners. Their overall risk of acquiring HIV is higher with male partners. Risk perception is associated with HIV knowledge, sexual risk and preventive behaviours. This synthesis aimed to summarize existing data about HIV knowledge and perceived HIV acquisition risk regarding sex with men and with women in MSM in SSA. Methods: We conducted a systematic literature review of MSM's relationships with women in SSA (PROSPERO-CRD42021237836). Quantitative and qualitative data related to MSM's perceived risk from sex with men and with women and HIV knowledge (published up to 2021) were selected and synthesized. Results: Twenty studies were selected. More MSM perceived that the greatest risk of HIV acquisition came from heterosexual/vaginal sex than from homosexual/anal sex (53% vs. 15%; 51% vs. 39%; 42% vs. 8%; 27% vs. 25%; 43% vs. 11%; 23% vs. 13%; 35% vs. 16%, cumulative sample n = 4396, six countries). A higher proportion of MSM received preventive information on heterosexual HIV transmission than on homosexual transmission (79% vs. 22%; 94% vs. 67%; 54% vs. 19%; cumulative sample n = 1199, four countries). The qualitative synthesis (eight studies) highlighted biology-and behaviour-based misconceptions leading MSM to perceive lower or negligible HIV risk from sex with men, compared to sex with women. These misconceptions were partly fuelled by the predominant focus on heterosexual and vaginal HIV transmission in HIV prevention information. Discussion: Common misconceptions regarding sexual risk between men remain unaddressed by the heteronormative messaging of HIV prevention. Underestimation by MSM of their HIV acquisition risk with male partners can pose significant barriers to effective HIV preventive behaviours and strengthen the transmission risk from MSM to their female partners. Conclusions: Improving access of MSM to tailored HIV prevention information and tools that address their practices with male and female partners is crucial. Integrating messages about anal sex into broader public health initiatives, including sexual health programmes targeting the general population, is essential. Further research in diverse settings in SSA is necessary to gain a greater understanding of the drivers and implications of HIV risk perception in MSM.