Sexually transmitted infections (STIs) are major concerns to public health as they continue to be a great burden to individuals in developing countries. They mostly affect key populations, including men who have sex with men (MSM), partly attributable to their poor health seeking behavior yet little attention has been given to them. Understanding the factors driving the prevalence in key population is crucial for prevention. This study investigated the prevalence of sexually transmitted infections and associated risk factors among men who have sex with men in Kisumu, Kenya. This analytical cross sectional study used data collected between January and December 2021 from 737 MSM enrolled at the Anza Mapema drop-in center, a dedicated clinic in Kisumu, providing prevention interventions for MSM. It involved abstraction of data from medical records of the 737 MSMs. Quantitative data was summarized using descriptive statistics, statistical differences between categorical variables assessed using the Chi-square test, and the factors associated with STI prevalence identified using logistic regression model. All analysis was done using SPSS version 23. Majority (450, 61.1%) of the MSM were aged 18-25 years and 83(11.5%) had a positive HIV status. Over half (404, 54.8%) of them preferred receptive/ bottom method of sexual intercourse, 154 (20.9%) preferred insertion/top, while 166(22.5%) preferred both methods. In this study, twenty percent 151(20.5%) of MSM had STI symptoms. Painful micturition (dysuria) (91,12.57%) urethral discharge (36, 4.97%) and genital sores (27, 3.73%) were the common STI symptoms. Secondary education level (adjusted odds ratio (AOR) = 0.48, 95% confidence interval: 0.3–0.755, P = 0.001), positive HIV status(adjusted odds ratio (AOR) = 1.95, 95% confidence interval: 1.16–3.29, P = 0.011), receptive sex(adjusted odds ratio (AOR) = 0.51, 95% confidence interval: 0.322–0.810, P = 0.004), lack of condom use(adjusted odds ratio (AOR) = 0.55, 95% confidence interval : 0.358– 0.864, P = 0.009), and experience of a condom break(adjusted odds ratio (AOR) = 1.68, 95% confidence interval : 1.115–2.548, P = 0.013) were the significant factors associated with STI symptoms among the MSM in Kisumu Kenya. In Kisumu, Kenya, 20% of MSM have STI and their high prevalence is linked to positive HIV status, secondary education level, and lack of condom use. Preventive measures such as regular screening, health education, and condom provision and treatment are necessary.