Background Chronic kidney disease (CKD) is defined as decreased glomerular filtration rate (GFR) of less than 60 mL/min per 1.73 m2 for more than 3 months, with or without kidney damage; or functional or structural abnormalities of the kidneys with or without decreased GFR. CKD is a recognized global public health problem whose effects are felt across different socioeconomic. It directly resulted in an estimated 1.23 million deaths in 2017. The objective of this study was to determine the prevalence and associated factors with chronic kidney disease.Methods A cross-sectional was conducted in selected hospitals in Kigali, Rwanda, using a structured questionnaire to collect data on sociodemographic factors and prevalence-morbidities and associated factors such as hypertension, diabetes mellitus, anemia, acute kidney disease, malaria antecedent, metabolic disease, heart disease, over-counter medication, traditional hypokalemia. A total sample size, which was 87 participants was selected from the inpatients using a simple random sampling technique selecting the study participants in the different medical wards of each hospital from January to March 2023. Data were entered into SPSS, coded, recorded, and analyzed in SPSS version 29 was used. Bivariate and multivariate analysis was conducted to analyze the sociodemographic characteristics, and factors association between variables and CKD. Adjusted odds ratio and 95% confidence level were reported. P-Value < 0.05 was used to declare statistical significance.Results A total of 87 inpatients in the medical ward at the university teaching of the Hospital of Kigali (CHUK) and King Faisal Hospital in Kigali were included in this study, and the prevalence of CKD was 20%. The co-morbidity diseases such as hypertension were represented by 58.6%, diabetes mellitus was 40.4% of study participants, around 36.8% of the participants had anemia, and the patients with acute kidney disease comorbidity 32.2%. Diabetes mellitus, hypertension, and malaria antecedent were significant with AoR:11.264 (2. 2.642–18.546); 6.215 (3.112–22.543); 4.112(1.724–14.254) and p < 0.001. Acute kidney disease, over-the-counter medication, and longer sickness periods were also significant with p < 0.05.Conclusion This study shows that the prevalence of CKD was 20%. The co-morbidity diseases such as hypertension were represented by 58.6%, diabetes mellitus was 40.4% of study participants, around 36.8% of the participants had anemia, and the patients with acute kidney disease comorbidity 32.2%. Diabetes mellitus. This study recommends the Ministry of Health in Rwanda and international partners should increase health education/health promotion for health workers and decrease the risk of developing serious CKD. Community-based public health education should be promoted to increase the knowledge and perception of better assessing and preventing disease, especially non-communicable diseases. The Ministry of Health must be preparing periodic campaigns through media, seminars, and workshops for the healthcare providers and patients who are involved.