Early life stress such as physical abuse, trauma or neglect during a critical period of development can elicit negative long-lasting effects on health. Neonatal maternal deprivation (MD) is a stressful event capable of triggering structural and neurobiological changes in Central Nervous System (CNS) development during proliferative and migratory cell differentiation. In this study, we investigated the maternal behavior of lactating rats submitted to protocol of chronic neonatal maternal deprivation (MD) during postnatal day (PND) 1 until 10. We analyzed the effects of the MD in the olfactory memory and cellular proliferation and differentiation in the hippocampus and olfactory bulb in Wistar rat pups on 7, 11 and 21 days postpartum. Analysis in active neurons, cellular differentiation and proliferation, were marked and evaluated by flow cytometry in tissue samples of hippocampi and olfactory bulb. Our results demonstrated an increase in maternal behavior immediately after dam's return to the home-cage in MD group compared to the non-deprived group. In addition, MD pups spent more time (higher latency) to identify the nest odor in comparison to the non-deprived rat pups in the olfactory learning task and showed a significant delay in the neural differentiation and proliferation in the hippocampus and olfactory bulb. These results reveal that disruptions in the mother-infant bonding by the MD induce changes in maternal behavior and interaction with the offspring that could be leading to delayed CNS development and significant impairment in offspring's olfactory learning.