Introduction Previous surveys of male sex workers (MSW) in sub-Saharan Africa have not fully documented the HIV and sexually transmitted infections (STIs) rates and vulnerabilities by age category. Methods The bio-behavioral survey of MSW in Nairobi, Kenya, utilized respondent-driven sampling to recruit MSW. Structured interviews captured MSW's behavioral aspects, and biological tests for HIV and other STIs. Results Analysis of the two age categories, 18–24 years (younger MSW) and 25 years and above (older MSW), shows that of all participants, a significantly higher proportion of younger MSW (59.6% crude, 69.6% RDS-adjusted) were recruited compared to older MSW (40.4% crude, 30.4% RDS-adjusted, P < 0.001). Young male sex workers were more likely to report multiple sexual partnerships in the last 12 months and had multiple receptive anal intercourses (RAI) acts in the last 30 days than older MSW: 0–2 RAI acts (20.6 vs. 8.6%, P = 0.0300), 3–5 RAI acts (26.3 vs. 11.5, P < 0.001), and >5 RAI acts (26.3 vs. 11.5%, P < 0.01). Furthermore, younger MSW were significantly more likely to have 3–5 insertive anal intercourse (IAI) with a regular male sex partner in the last 30 days than older MSW (24.3 vs. 8.0%, P < 0.01). Younger MSW were also more likely to report other STIs [28.5% (95% CI: 19.1–40.4%)] than older MSW [19.0% (95% CI: 7.7–29.2%)]. However, older MSWs were more likely to be infected with HIV than younger MSW (32.3 vs. 9.9 %, P < 0.01). Conclusions Owing to the high risk sexual behaviors, HIV and STIs risks among younger and older MSW, intensified and targeted efforts are needed on risk reduction campaigns and expanded access to services.