Background: Accurate glomerular filtration rate estimation (eGFR) is essential for managing pediatric kidney transplant recipients. Given the physiology of pediatric patients receiving adult-donor kidneys, identifying the most appropriate plasma creatinine (PCr)-based formula—pediatric or adult-specific—is crucial. Methods: This cross-sectional study included pediatric kidney transplant recipients (age 1–18 years) who received adult-donor kidneys. We compared agreement thresholds of various pediatric and adult PCr-based GFR equations with CKiD 2012 combined PCr‒cystatin C (PCr-CystC) equation via intraclass correlation coefficients (ICCs), concordance correlation coefficients (CCCs), total deviation index (TDI), P30 performance metric (P30), Bland–Altman plots, and receiver-operating characteristic (ROC) analysis. Correlation between CKiD under 25 (U25) PCr–CystC and reference CKiD 2012 equation was also evaluated. Results: One hundred twenty samples were collected from 23 recipients (mean age = 14.2 ± 3.4 years) and donors (mean age = 31.7 ± 10.0 years). Schwartz–Lyon equation demonstrated the highest performance with the reference (ICC = 0.913, CCC = 0.911, TDI = 14.0 mL/min/1.73 m 2 , P30 = 99.2%). U25 (ICC = 0.922, CCC = 0.882, P30 = 93.3%), full age spectrum (FAS)-height (ICC = 0.897, CCC = 0.877, P30 = 96.7%), and Bedside Schwartz equations (ICC = 0.850, CCC = 0.819, P30 = 89.2%) showed comparable performance. Bland–Altman plots revealed proportional bias ( p < 0.05), leading to ROC analysis, which identified eGFR < 70 mL/min/1.73 m 2 for Schwartz–Lyon, U25, and FAS-height, and < 60 mL/min/1.73 m 2 for Bedside Schwartz as optimal agreement thresholds, beyond which each equation showed increased bias. Subgroup analyses also showed better performance in patients aged 10–18 years. Additionally, U25 PCr-CystC equation showed excellent agreement with the reference (ICC = 0.993, CCC = 0.990, P30 = 100%). Conclusions: Schwartz–Lyon equation demonstrated the highest performance among PCr-based equations with the reference in pediatric kidney transplant recipients, particularly when eGFR was < 70 mL/min/1.73 m 2 and in patients aged 10–18 years. U25 PCr-CystC equation showed best overall agreement with the reference and should be preferred where CystC measurement is feasible. Graphical A higher resolution version of the Graphical abstract is available as Supplementary information.