In developing countries, prenatal lipid-based nutrient supplements were shown to increase birth size, however the mechanism of this effect remains unknown. Cord blood hormone concentrations are strongly associated with birth size. Therefore, we hypothesize that lipid-based nutrient supplements increase birth size through a change in the endocrine regulation of fetal development. We compared the effect of daily prenatal lipid-based nutrient supplements (LNS) with multiple micronutrient tablets on cord blood hormone concentrations using a randomized controlled design including 197 pregnant women from rural Burkina Faso. Insulin-like growth factors I and II, their binding proteins IGFBP-1 and IGFBP-3, leptin, cortisol and insulin were quantified in cord sera using immunoassays. LNS was associated with higher cord blood leptin mainly in primigravidae (+57%; P = 0.02) and in women from the highest tertile of body mass index at study inclusion (+41%; P = 0.02). We did not find any significant LNS effects on other dosed cord hormones. The observed increase in cord leptin was associated with a significantly higher birth weight. Cord sera from Small-for-Gestational Age newborns had significantly lower median Insulin-Like Growth Factor I (-9 µg/L; P = 0.003), Insulin-Like Growth Factor II (-79 µg/L; P = 0.003), IGFBP-3 (-0.7 µg/L; P = 0.007) and leptin (-1.0 µg/L; P = 0.016) concentrations, but higher median cortisol (+18 µg/L; P = 0.037) concentrations compared to normally grown newborns. Prenatal lipid-based nutrient supplementation resulted in increased cord leptin concentrations in primigravidae and mothers with lower body mass index at study inclusion. The elevated leptin levels could point towards a higher neonatal fat mass.