Inflammatory Bowel Disease (IBD) is a group of chronic and recurrent inflammatory diseases characterized by prolonged inflammation of the intestinal tract. Although it has been proven that the immune system plays a crucial role in the pathogenesis of IBD, a defective intestinal epithelium is also responsible for chronic inflammation, hence causing an over-activation of the immune response. For this reason, a therapeutic approach that acts by improving impaired intestinal homeostasis could ensure a greater therapeutic efficacy in IBD. Mitogen-activated protein kinases (MAPKs) signaling pathways may be involved in the pathogenesis of IBD. It has been demonstrated that the inhibition of mitogen-activated protein kinase kinase 1 (MEK1) may be a potential treatment against IBD since it may restore the normal epithelial function and reduce apoptosis of intestinal epithelial cells (IECs). New therapeutic strategies are emerging including small molecules such as microRNAs (miRNAs). In this study, we aimed to demonstrate that miR-369-3p was able to modulate the MEK/ERK signaling pathway. As reported by in silico analysis, miR-369-3p was capable of pairing the 3'UTR of the MAP2K1 gene. In vitro analysis demonstrated that mimic transfection with miR-369-3p in epithelial cells downregulated the expression of MEK1, reduced the activation of ERK signaling, and modulated apoptosis of epithelial cells in response to TNF-α. Moreover, miR-369-3p significantly decreased the release of pro-inflammatory cytokine IL-8. These results support the potential of miR-369-3p to prevent apoptosis of IECs, responsible for a persistent inflammatory condition in IBD, highlighting its application value in the treatment of inflammatory disorders.