To compare the pattern of serum FGF23 levels in pediatric renal transplant recipients and GFR‐matched controls. We performed a cross‐sectional matched pair study in 19 stable pediatric renal transplant recipients and 19 GFR‐matched controls with native CKD. After assessment for normal distribution, demographic and bone metabolism parameters were compared with Student’s t‐test, Wilcoxon’s matched pairs (for non‐normal distribution) test, and correlation analysis. The groups were comparable for anthropometric parameters, cystatin C eGFR (71.10 ± 37.28 vs. 76.11 ± 26.80 mL/min/1.73 m2), cystatin C, urea, creatinine, intact PTH, pH, CRP, alkaline phosphatase, phosphate, calcium, ionized calcium, FGF‐23 (63.44 [IQR 38.42, 76.29], 49.92 [IQR 42.48, 76.97]), albumin, and urinary calcium/creatinine ratio. The renal transplant patients had significantly lower 25‐(OH) vitamin D levels (66.63 ± 17.54 vs. 91.42 ± 29.16 ng/mL), and higher 1,25‐(OH)2 vitamin D levels (95.78 ± 34.54 vs. 67.11 ± 35.90 pm). FGF‐23 levels correlated negatively with cystatin C eGFR (r = −0.3571, p = 0.02770) and positively with PTH (r = 0.5063, p = 0.0026), but not with serum phosphate (r = 0.2651, p = 0.1077). We conclude that the increase in FGF23 levels with GFR decline in pediatric renal transplant patients remains similar to that in the patients with CKD. The relationship between FGF23 and serum vitamin D needs further evaluation.