The Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equation is the most commonly used equation for estimated glomerular filtration rate (eGFR). Recently, the European Kidney Function Consortium (EKFC) announced a full-age spectrum equation, and the CKD-EPI announced the CKD-EPI refit equations (CKD-EPI-R). We compared CKD-EPI, EKFC, and CKD-EPI-R equations in a large-scale Korean population and investigated their potential implications for CKD prevalence. In a total of 106,021 individuals who received annual check-ups from 2018 to 2020, we compared the eGFR equations according to the Clinical and Laboratory Standards Institute guidelines. Weighted kappa (κ) agreement was used to compare the potential implications for CKD prevalence across the equations. The median value of eGFR tended to increase in the order of EKFC, CKD-EPI, and CKD-EPI-R equations (92.4 mL/min/1.73 m2, 96.0 mL/min/1.73 m2, and 100.0 mL/min/1.73 m2, respectively). The EKFC and CKD-EPI-R equations showed a very high correlation of eGFR and good agreement for CKD prevalence with CKD-EPI equation (r = 0.98 and 1.00; κ = 0.80 and 0.82, respectively). Compared with the CKD-EPI equation, the EFKC equation overestimated CKD prevalence (3.5%), and the CKD-EPI-R equation underestimated it (1.5%). This is the first study comparing CKD-EPI, EKFC, and CKD-EPI-R equations simultaneously. The EKFC and CKD-EPI-R equations were statistically interchangeable with CKD-EPI equations in this large-scale Korean population. The transition of eGFR equations, however, would lead to sizable changes in the CKD prevalence. To improve kidney health, in-depth discussion considering various clinical aspects is imperative for the transition of eGFR equations.