Stress during prenatal period can affect the young ones, increasing the risk of aberrations in gut-brain of neonates during critical developmental periods and serves as a risk factor for postnatal pathologies. Compelling data from animal studies has shown that gestational stress-induced hyperactivation of the hypothalamic-pituitary-adrenal (HPA) axis, marked by excessive corticosterone (CORT) release, underlies profound and lasting developmental deficits in the offspring. It is well-established that stress during the gestational period disrupts gut and brain homeostasis in the F1 generation of Wistar rats. However, morin (3, 5, 7, 2', 4'-pentahydroxyflavone), a plant flavonoid, exerts neuroprotective and antioxidant potential which could be beneficial in management of prenatal stress (PNS). Hence, this study was designed to evaluate the mitigatory potential of morin against the detrimental effects of prenatal stress, including the early onset of apoptosis in the gut and brain of the F1 offspring. Morin treatment to the stressed dams significantly improved HPA axis mediated oxidative stress and gut & brain barrier permeabilities. Furthermore, morin, due to its redox balancing and anti-inflammatory properties, prevented early onset of apoptosis, maintained the histoarchitecture and functions of gut & brain in F1 progeny. These findings provide a favourable research basis that morin administration during gestational period can significantly help in regulation of stress induced transgenerational gut-brain axis pathologies.