Cold burn wounds differ in their pathophysiological spectrum as compared to other types of burn wounds. These wounds have prolonged devastating effects on the body including hypertrophic scars, contracture, and necrosis. Mesenchymal stem cells (MSCs) are considered promising candidates for the complete regeneration of burn wounds. However, transplanted MSCs face the challenge to survive under the harsh tissue conditions. Preconditioning of MSCs with bioactive compounds may enhance their survival and regenerative potential for use in clinical applications. Bioactive compounds of Melia azedarach are well known for their potential role in treating different types of skin wounds due to their anti-inflammatory, anti-viral, anti-cytotoxic, and anti-oxidative properties. This study aims to evaluate the synergistic effects of human umbilical cord derived MSCs (hUC-MSCs) after preconditioning them with bioactive compounds of M. azedarach (quercetin and rutin) for cold induced burn wounds. Human umbilical cord MSCs (hUC-MSCs) were characterized based on their specific cell surface markers and treated with 20 μM of quercetin or rutin. In vitro scratch assay was performed to measure cell migration and wound closure. In vivo cold burn wound model was developed via direct exposure of the dorsal rat skin to liquid nitrogen. hUC-MSCs were subcutaneously transplanted next day of burn wound induction and wound was examined at different time points corresponding to the wound healing phases (days 3, 7, and 14). The regenerative potential of preconditioned hUC-MSCs was assessed in different groups; control (treated only with hUC-MSCs), and treated groups (quercetin or rutin treated hUC-MSCs). Healing potential and wound closure were evaluated by histological, gene expression, and immunohistochemical analyses of the wound tissues before and after treatment. Scratch assay exhibited enhanced cell migration towards wound closure in the treated groups as compared to the control. Macroscopic examination of the wound revealed scab formation at day 14 in control, whereas scab was detached and the wound tissue was remarkably remodeled in the treated groups. Comparison between the treated groups showed that burn wound treated with quercetin significantly increased healing potential than the rutin treated MSCs. Histological findings showed enhanced regeneration of skin layers along with hair follicles in the quercetin group, while increased neovascularization was noted in both treatment groups. Gene profile of wound healing mediators illustrated significant upregulation of IL-5, IL-4, GPX-7, TXNRD-2, PRDX, VEGF, and FGF and downregulation of inflammatory cytokines IL-1β and IL-6. In conclusion, synergistic effect of hUC-MSCs and bioactive compounds of M. azedarach enhances wound healing by reducing the inflammation, mitigating oxidative stress and enhancing neovascularization. The study findings will aid in designing more effective treatment options for cold burn wounds.