Neurogenic bladder due to myelomeningocele (MMC) is a significant risk factor for chronic kidney disease in children. Cystatin C (CysC) is a more accurate GFR marker than creatinine as it is unaffected by muscle mass but may be influenced by fat mass and BMI. This study evaluates: (1) GFR measurement accuracy using CysC and creatinine in MMC-related neurogenic bladder, (2) the relationship between body composition via bioelectrical impedance analysis (BIA) and renal parameters, and (3) the use of BIA for non-invasive GFR and body composition assessment. Forty children (median age 9.96years) underwent serum creatinine, CysC testing, and BIA measurements. We assessed age, sex, spinal lesion level, anthropometric measurements, BMI, and activity using Hoffer's scale. GFR was calculated using five creatinine-based formulas, three CysC-based, and three combining CysC and creatinine, including BIA GFR as an alternative approach. Creatinine-based GFR estimates were significantly higher than CysC-based GFR. Although only 30% of MMC patients met the traditional BMI criteria for overweight/obesity, 62.5% were obese based on BIA-measured body fat percentage. Significant differences were found in CysC and CysC-based GFR equations within BMI and fat mass groups. Positive correlations were observed between CysC and body weight, BMI percentiles, body fat mass and fat-to-muscle ratio. Muscle mass positively correlated with creatinine. BIA-determined fat mass percentage is a more sensitive obesity indicator than BMI in MMC patients. CysC levels and CysC-based GFR equations are influenced by body fat mass, requiring consideration of adiposity to avoid misestimating renal impairment.