Background: Hyperbaric oxygen treatment (HBOT) has been used for more than a decade to treat diverse diseases like diabetic foot ulcers and ischemic injuries. More recently, HBOT has been reported to modulate proliferation of neural and intestinal stem cell populations, but the molecular mechanisms underlying these effects are not completely understood. Objective: In this study we aimed to determine HBOT stem cell modulation by evaluating in particular the role of the mTOR complex 1 (mTORc1), a key regulator of cell metabolism that modifies its activity depending on oxygen levels, as a potential mediator of HBOT in murine intestinal stem cells (ISCs). Methods: Mouse were exposed to 10 or 20 HBOT sessions and the proliferation of the ISCs were analyzed by immunofluorescence or immunohistochemistry using the specific ISCs marker, Olfm4. The regulation of HBOT and mTORc1 pathway was analyzed through S6K1 phosphorylation by western-blot and through the inhibition by rapamycin. Results: We discovered that acute HBOT can increase proliferation of ISCs in a synchronous fashion without affecting the animal’s oxidative metabolism. Noteworthy, the mTORc1 inhibitor rapamycin also increases the proliferation of ISCs. This effect has been attributed to its capacity to mimic a caloric restriction (CR). Interestingly, the combination of HBOT and rapamycin does not have a synergic effect. Nevertheless, HBOT can recover rapamycin induced mTORc1 inhibition, possibly acting through a competitive modulation on mTORC1. Conclusions: Collectively, our results suggest that HBOT proliferative effect on ISCs is modulated by mTORc1 signaling representing a promising new approach to treat intestinal conditions.