(1) Background: Accurate estimation of the glomerular filtration rate (eGFR) is essential for the early detection of chronic kidney disease (CKD), targeted interventions, and ongoing monitoring. Although various equations for calculating eGFR exist, comparative studies on eGFR levels and the impact of these equations on CKD prevalence are limited in the Korean population. (2) Methods: We compared eGFR levels calculated using seven equations and investigated the prevalence of CKD through a retrospective analysis of the data from Korean adult patients who visited local clinics and hospitals and underwent simultaneous serum creatinine (Cr) and cystatin C (Cys-C) measurements. The equations analyzed were: 2006 MDRD, 2009 CKD-EPI Cr, 2012 CKD-EPI Cys-C, 2012 CKD-EPI Cr & Cys-C, 2021 CKD-EPI Cr, 2021 CKD-EPI Cr & Cys-C, and 2021 EKFC. (3) Results: This study included 6688 Korean patients (3736 men and 2952 women; median age: 61.4; IQR: 47.2–73.4). Among the equations, the median eGFR levels were the highest when using the 2021 CKD-EPI Cr & Cys-C equation (85.1 mL/min/1.73 m2) and the lowest when using the 2006 MDRD equation (73.4 mL/min/1.73 m2). The highest prevalence of decreased eGFR < 60 mL/min/1.73 m2 (equivalent to or worse than G3a CKD) was noted with the 2012 CKD-EPI Cys-C equation (32.4%), while the lowest was with the 2021 CKD-EPI Cr equation (22.9%), resulting in a maximum prevalence difference of 9.5%. (4) Conclusions: The prevalence of CKD varies based on the eGFR equation used and the patient’s age. Equations that include Cys-C may identify a larger number of patients with decreased kidney function.