Chronic kidney disease (CKD) is a prevalent global health issue that impacts around 10% of the global population with significantly higher prevalence rates observed in specific regions like Sub-Saharan Africa (13.4%), Eastern Africa (14%), and particularly in Rwanda with 20%. Little information is known about the magnitude of CKD and its associated factors in people with hypertension particularly in Rwanda. Consequently, the primary goal of this study is to ascertain the prevalence of chronic kidney disease and explore the factors associated with it in individuals with hypertension attending Kigeme District Hospital. The research adopted a cross sectional design, recruiting 271 participants through a simple random technique. Structured open-ended questionnaires were used for interviews. The study used univariate analysis to measure the prevalence of CKD and bivariate and multivariate analysis to explore associations between dependent and independent variables using fisher exact tests. Both research and medical ethics including privacy and confidentiality of the respondents was respected. The study findings revealed that 14.4% of respondents were affected by chronic kidney disease (CKD), highlighting its prevalence within the surveyed population. In contrast, the vast majority, comprising 85.6% of respondents, were not suffering from this condition. Bivariate analysis identified three comorbidity and behavioral factors significantly associated with CKD: diabetes, hepatitis C, and HIV status, with Fisher exact test values ranging from 4.625 to 6.315 and all p-values < 0.001. Additionally, uncontrolled hypertension and BMI were found to be significant, with p-values ranging from 0.012 to 0.032. Uncontrolled hypertension emerged as a notable associated factor, with individuals being eleven times more likely to have CKD (Adjusted Odds Ratio [AOR] = 11.105, 95% Confidence Interval [CI]: 1.197-19.061, p = 0.03). Hypertension duration exceeding 5 years was also significant predictors of CKD, with adjusted odds ratios of 12.149 (95% CI: 1.975-74.653, p = 0.007) and 15.558 (95% CI: 8.090-22.273, p < 0.001), respectively. Furthermore, diabetes mellitus and family history of CKD were also significant, with p-values < 0.05. After controlling confounders in multivariate analysis, only uncontrolled hypertension and duration of hypertension exceeding 5 years were significantly associated with CKD. This study concluded that comorbidities such as hepatitis C and HIV were only linked with CKD by bivariate analysis. Moreover, hypertension duration more than five years, diabetes and uncontrolled hypertension were both associated with chronic kidney disease among patients attending Kigeme hospital and recommended policymakers and health officials create policies and preventive measures that could proactively support patient’s education framework, early detection and early management of hypertension