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Abstract Background Female sex workers (FSW) and men having sex with men (MSM) in Kenya have high rates of HIV infection. Following a 2015 WHO recommendation, Kenya initiated national scale-up of pre-exposure prophylaxis (PrEP) for all persons at high-risk. Concerns have been raised about PrEP users' potential changes in sexual behaviors such adopting condomless sex and multiple partners as a result of perceived reduction in HIV risk, a phenomenon known as risk compensation. Increased condomless sex may lead to unintended pregnancies and sexually transmitted infections and has been described in research contexts but not in the programmatic setting. This study looks at changes in condom use among FSW and MSM on PrEP through a national a scale-up program. Methods Routine program data collected between February 2017 and December 2019 were used to assess changes in condom use during the first three months of PrEP in 80 health facilities supported by a scale-up project, Jilinde. The primary outcome was self-reported condom use. Analyses were conducted separately for FSW and for MSM. Log-Binomial Regression with Generalized Estimating Equations was used to compare the incidence proportion (“risk”) of consistent condom use at the month 1, and month 3 visits relative to the initiation visit. Results At initiation, 69% of FSW and 65% of MSM reported consistent condom use. At month 3, this rose to 87% for FSW and 91% for MSM. MSM were 24% more likely to report consistent condom use at month 1 (Relative Risk [RR], 1.24, 95% Confidence Interval [CI], 1.18–1.30) and 40% more likely at month 3 (RR, 1.40, 95% CI, 1.33–1.47) compared to at initiation. FSW were 15% more likely to report consistent condom use at the month one visit (RR, 1.15, 95% CI, 1.13–1.17) and 27% more likely to report condom use on the month 3 visit (RR 1.27, 95% CI, 1.24–1.29). Conclusion Condom use increased substantially among both FSW and MSM. This may be because oral PrEP was provided as part of a combination prevention strategy that included counseling and condoms but could also be due to the low retention rates among those who initiated.