Abstract Background and Aims Chronic kidney disease (CKD) represents a significant and growing global health challenge, especially among aging populations. Despite declines in mortality from other non-communicable diseases, CKD-related mortality has remained stable, underscoring the need for enhanced management strategies. Primary care physicians play a crucial role in early detection and appropriate intervention. Understanding geographical variation in CKD prevalence and incidence is essential for clinicians and policy makers, informing the development of targeted interventions and resource allocation strategies. This study investigates CKD in Denmark, assessing variations in prevalence and incidence across rural and urban areas. Method This nationwide cohort study included all Danish residents aged ≥18 years as of January 1, 2019. Patients with CKD were identified using measurements of eGFR from the Register of Laboratory results for Research. CKD was defined according to KDIGO as at least two reported outpatient eGFR <60 ml/min/1.73 m2 at least 90 days apart. Population characteristics, CKD prevalence and CKD incidence were analyzed by urbanicity of residence municipality (capital, large city, provincial, sub-rural and rural municipalities). Two different models were used to estimate incidence rates; a crude model and a model using propensity score weighting for standardization, accounting for age and sex. Results The study included 4,466,041 Danish residents. There was variation in population characteristics and CKD incidence between urban and rural areas such as CKD prevalence, hypertension, diabetes, and Charlson Comorbidity Index. The crude model showed geographical differences in CKD incidence rates varying between 7.4 and 12.8 per 1,000 person-years in large city municipalities and rural municipalities, respectively. The standardized model showed less variation, with incidence rates ranging from 9.2 to 10.5 cases of CKD per 1,000 person years. Conclusion The study illuminates geographical variations in CKD prevalence and incidence across Danish rural and urban municipalities. After standardization for age and sex, there was only minor variation in incidence rates of CKD, suggesting that variation could largely be explained by differences in demographic, highlighting the need for targeted interventions accounting for diverse population characteristics in different geographic regions.