Introduction: Atrial fibrillation (AF) and CKD are commonly coexisting conditions. However, data on epidemiology of AF in patients with CKD stage 4–5 is scarce. Methods: We prospectively enrolled 210 consecutive non-dialysis patients with CKD stage 4–5 between 2013 and 2017. Follow-up data on AF incidence along with medical history, laboratory tests, and echocardiography at baseline were gathered. Results: At baseline, mean age was 62 years, estimated glomerular filtration rate 12.8 mL/min, and 73/210 (34.8%) participants were female. Altogether, 41/210 (19.5%) patients had a previous diagnosis of AF. After median follow-up of 46 [IQR 27] months, new-onset AF occurred in 33/169 (19.5%) patients (69.9 events/1,000 person-years). In the Cox proportional hazard model, age >60 years (HR 4.27, CI 95% 1.57–11.64, p < 0.01), elevated troponin T (TnT) >50 ng/L (HR 3.61, CI 95% 1.55–8.37, p < 0.01), and left atrial volume index (LAVI) >30 mL/m<sup>2</sup> (HR 4.82, CI 95% 1.11–21.00, p = 0.04) were independently associated with the incidence of new-onset AF. Conclusion: The prevalence and incidence of AF was markedly high in this prospective study on patients with CKD stage 4–5. Elevated TnT and increased LAVI were independently associated with the occurrence of new-onset AF in patients with severe CKD.