BACKGROUND Human mesenchymal stromal cells (MSCs) possess regenerative potential due to pluripotency and paracrine functions. However, their stemness and immunomodulatory capabilities are sub-optimal in conventional two-dimensional (2D) culture. AIM To enhance the efficiency and therapeutic efficacy of MSCs, an in vivo-like 3D culture condition was applied. METHODS MSCs were cultured on polystyrene (2D) or in a gellan gum-based 3D system. In vitro, prostaglandin-endoperoxide synthase 2, indoleamine-2,3-dioxygenase, heme oxygenase 1, and prostaglandin E synthase gene expression was quantified by quantitative real-time polymerase chain reaction. MSCs were incubated with lipopolysaccharide (LPS)-treated mouse splenocytes, and prostaglandin E2 and tumor necrosis factor-alpha levels were measured by enzyme linked immunosorbent assay. In vivo, LPS was injected into the lateral ventricle of mouse brain, and MSCs were administered intravenously the next day. Animals were sacrificed and analyzed on days 2 and 6. RESULTS Gellan gum polymer-based 3D culture significantly increased expression of octamer-binding transcription factor 4 and Nanog homeobox stemness markers in human MSCs compared to 2D culture. This 3D environment also heightened expression of cyclooxygenase-2 and heme-oxygenase 1, enzymes known for immunomodulatory functions, including production of prostaglandins and heme degradation, respectively. MSCs in 3D culture secreted more prostaglandin E2 and effectively suppressed tumor necrosis factor-alpha release from LPS-stimulated splenocytes and surpassed the efficiency of MSCs cultured in 2D. In a murine neuroinflammation model, intravenous injection of 3D-cultured MSCs significantly reduced ionized calcium-binding adaptor molecule 1 and glial fibrillary acidic protein expression, mitigating chronic inflammation more effectively than 2D-cultured MSCs. CONCLUSION The microenvironment established in 3D culture serves as an in vivo mimetic, enhancing the immunomodulatory function of MSCs. This suggests that engineered MSCs hold significant promise a potent tool for cell therapy.