Introduction: Feeling stressed is common during pregnancy and some pregnant women experience some level of anxiety. Prenatal Stress alters the activity of the hypothalamic-pituitary-adrenal axis of infants and affects glucocorticoid receptors in the hippocampus. Many researchers have described the deacetylase histone inhibitors as a new group of drugs that improve the long-term memory formation. These drugs can improve memory in normal animals as well as in animal with brain disorders. The objective of this study was to study the neuroprotective effects of sodium butyrate, as a histone deacetylase inhibitor, on improving cognitive functions in new born rats born of stressed mother. Materials and Methods: 15 pregnant female rats received foot shock (5 times per day and at the current intensity of 1 mA and frequency of 50 MHz with 3 Minutes intervals for 2 seconds) between day 12 to day 18 of pregnancy. Infants born to these mothers were classified in three treatment groups, including Shock, shock + sodium butyrate 0.35 grams per liter, and shock + sodium butyrate 3.5 grams per liter. Infants born to mothers who were not under any shock during their pregnancy were used as the control group. To assess the working memory, Y maze test was performed on postnatal 30 and 60 days. Then, serum level of neural growth factor was measured by ELISA. Results: Periodic behaviors were significantly decreased in shock group. A significant increase in the group receiving sodium butyrate was observed compared to the control group. Besides, sodium butyrate administration increased serum level of neural growth factor. Working memory and serum level of neural growth factor in foot shock stress model were decreased. Conclusion: Administration of sodium butyrate revealed a neuroprotective effect probably via increase of neural growth factor and may improve the cognitive function of infants with prenatal stress.