Endoplasmic reticulum (ER) stress is induced in various physiological or pathological conditions. During embryonic development, ER stress occurs in order to organize neuronal architecture. Melatonin, pineal hormone, has roles for neuronal protection as well as cell death inhibition. The purpose of this study was to confirm the effect of melatonin treatment (10 mg/kg/day) into the Sprague Dawley rats under conditioned photoperiod (L/D, LL, and DD) on ER stress during brain development. As a result, maternal body weight was lower in the melatonin‐treated rats (MT) than control rats (Con) in LL as well as DD group at embryonic day 20 (P<0.05). Body weight of pups was higher in MT than Con group under LD and DD condition, whereas lowest in MT group under LL condition (P<.05). mRNA expression of eIF2a, PERK and XBP‐1 were significantly decreased in MT compared to Con group at embryonic day 20 (P<.05) Interestingly, expression of LC3 mRNA was significantly decreased in MT group of LL and DD condition at the same time point (P<0.05). Taken together, endogenous and/or exogenous melatonin reduced autophagy activation as well as ER stress during embryonic development suggesting that melatonin is beneficial to formation of nervous system.