Background Safe male circumcision is a medical procedure believed to reduce the risk of female to male HIV transmission. However, its‘ uptake is still low in some communities due to a several factors. In this study, the prevalence and factors associated with the uptake of safe male circumcision among youth living in fishing villages of Siaya County was done. Results from this study may be useful in advocating for strategies that may improve the uptake of safe male circumcision among the youths. Methods This was a cross sectional study on 228 youths. Data on uptake of safe male circumcision and factors associated with its uptake was obtained from the respondents using questionnaire-based interviews. Chi square tests were used to determine the association between the uptake of safe male circumcision and associated factors. P values and their 95 % confidence intervals were calculated. For all statistical tests a P-value of less than 0.05 was considered significant. Results The prevalence of uptake of safe male circumcision among the youth living in the lake side villages of Siaya County was 67%. Various factors were significantly associated with uptake of SMC; these included social demographic factors such as age, religion, marital status, type of housing, main source of income and monthly income. Awareness of SMC, source of information on SMC, knowledge on the benefits, and who influenced one to go for SMC, were significant predictors of SMC. Barriers associated with uptake of SMC and perceptions on the importance of SMC were the sociocultural factors significantly associated with uptake of SMC among the respondents. Conclusion and recommendations The prevalence of uptake of safe male circumcision among the youth living in the lake side villages of Siaya County was 67%. This percentage has not changed from the earlier reported prevalence of uptake of safe male circumcision in Nyanza (66%) by 2012, depicting stagnation in usage of the procedure. Therefore, County and national task forces should be setup to conduct robust sensitization campaigns that are focused on educating health workers,political and traditional leaders, youths and the media about safe male circumcision, its benefits and its relation to HIV prevention. This may promote the uptake of SMC services among the youth and older men. Additionally, circumcision services need to be more robust and tailored to fit the preferences of even the remaining population that is not circumcised. And leave should be issued and due compensation given to encourage the procedure.

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