Children with spina bifida (SB) face an elevated risk of obesity, which necessitates precise methods for assessing body composition to ensure effective weight management. Conventional measures like BMI are inadequate for this population because of variations in growth patterns and skeletal structure. Bioelectrical impedance analysis (BIA) is a method that offers a clearer picture of body composition, yet its use in children with SB remains underexplored. Conducted on 57 children with SB and 28 healthy controls, with a median age of 11 years, this study evaluated anthropometrics, including BMI and BIA-derived metrics. The Hoffer's scale to assess physical activity was applied in SB children. Results showed that while 32% of SB patients were classified as overweight or obese based on BMI, 62% exhibited high body fat percentage via BIA. Fat-free mass, muscle and fat mass, and fat-to-muscle ratio (FMR) differed significantly compared to the reference group. Non-ambulators showed a higher median body fat mass percentage (25.9% vs. 17.8%, p = 0.01) and FMR (0.92 vs. 0.44, p = 0.003) in comparison to the community walkers. In SB children, BIA-measured fat mass is a better obesity indicator than BMI. Non-ambulatory, SB patients with obesity had the highest FMR values, indicating a higher risk for metabolic syndrome.