Compelling data suggest that perturbations in microbial colonization of the gut in early‐life, influences neurodevelopment and adult brain function. If this is the case, then ensuring the growth of beneficial bacteria at an early age will lead to optimal brain development and maturation. We have tested whether feeding neonatal rats daily (from post‐natal days 3‐21) with a galacto‐oligosaccharide prebiotic (Bimuno®, BGOS) or a control solution, alters the levels of hippocampal N‐Methyl‐D‐Aspartate receptor (NMDAR) subunits (GluN1, GluN2A, GluN2B), synaptic proteins (synaptophysin, MAP2, and GAP43) and brain‐derived‐neurotrophic factor (BDNF), at post‐natal days 22 and 56. The administration of BGOS significantly elevated GluN2A subunits, synaptophysin and BDNF in the hippocampus of 22 day old rats. The effect was also observed on day 56 (26 days after the feeding ceased). The levels of all other proteins (GluN1, GluN2B, MAP2, GAP43) remained unaltered. Increased GluN2A, synaptophysin, BDNF, but not MAP2, may suggest that neonatal BGOS feeding alters neurotransmission rather than synaptic architecture. Although the functional consequences of our findings require further investigation, the current study confirms that the manipulation of gut bacteria in early‐life, has central effects that persist until at least young adulthood. Synapse 70:121–124, 2016. © 2016 Wiley Periodicals, Inc.