Introduction: The presence of apelin in hypothalamus indicates the potential role of this hormone in the balance of energy and food intake. According to apelin’ s protective role on obesity, this study was performed with aim to investigate the relationship between serum apelin-36 with mother's anthropometric indices at 18-24 months postpartum. Methods: In this nested case-control study, serum apelin-36 levels of 42 pregnant women was measured during 28-32 weeks of gestation and the first 24 hours after delivery using ELISA in 2014-2016. After delivery, the participants were divided in to two subgroups based on mode of delivery; vaginal delivery group and cesarean section group. Anthropometric indices were measured two times; third trimester of pregnancy and then 18-24 months after delivery. Data were analyzed by SPSS software (version 21) and independent t and paired t-test, Chi-square, regression, and Pearson correlation test. P<0. 05 was considered significant. Results: Mean of serum apelin-36 level after vaginal delivery had a nearly significant reduction compared with third trimester of pregnancy (P=0. 05). Serum level of apelin-36 after cesarean delivery had negative significant relationship with BMI (P = 0. 007, r =-0. 57) and waist circumference (P = 0. 003, r =-0. 62) at postpartum follow-up. Linear regression analysis revealed that serum apelin-36 after caesarian delivery was a significant independent predictors of BMI at postpartum follow-up (P< 0. 01). Apelin-36 had no significant relationship with anthropometric parameters in vaginal delivery group (P> 0. 05). There was no significant difference in mean of anthropometric indices between two groups including: total pregnancy weight gain (P = 0. 51), third trimester BMI (P = 0. 11), BMI (P = 0. 19), waist circumference (P = 0. 21), systolic (P = 0. 22) and diastolic blood pressure (P = 0. 34), weight retention (P = 0. 37) at postpartum follow-up. Conclusion: Maternal serum apelin-36 level had negative significant relationship with maternal body mass index and waist circumference in cesarean section group. However, this mechanism is not completely known.