The APLN T-1860C polymorphism (OR = 4.39, 95% CI = 1.25–15.28) and apelin concentration (OR = 0.45, 95% CI = 0.23–0.92) were significantly associated with obesity among female children (p < 0.05) only, after adjusting for potential covariates. Here, APLN is linked to obesity due to melanocortin 4 receptor deficiency.