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Mesenchymal stem cells (MSCs) have unique potentials, including migration and immunomodulation. Identification of the factors that enhance these activities can improve clinical applications of MSCs. This study aimed to investigate total antioxidant capacity (TAC) and migration potential of mouse MSCs exposed to thymoquinone (TQ) in vitro , and to examine the effect of TQ-treated MSCs on the expression of mouse immune cell markers. The results of total antioxidant capacity and wound healing assays showed that TQ increased the rate of MSCs TAC and migration in a dose- and time-dependent manner. The maximum TAC and migration were detected at 600 and 250 ng/ml of TQ, respectively. Functionally, the real-time PCR data analysis indicated that TQ induced c-Met and Cxcr4 expression and therefore, there may be a correlation between upregulation of these genes and increased MSCs migration. TQ also enhanced the up and down regulating impact of MSCs on Rorγt and Plzf expression and the expression of Tcf4 in mouse immune cells, respectively. Overall, this study declares that TQ increases the TAC of MSCs. It also proposes that TQ may, through activation of c-MET and CXCR4 signalling pathways, promote MSCs migration. TQ may also augment MSCs immunogenicity through its influence on the expression of genes involved in commitment of mouse immune system cells in vivo. • TQ increases total antioxidant capacity of MSCs. • TQ may promote MSCs migration by activating c-MET and CXCR4 signalling pathways. • TQ-treated MSCs induce Pax5 , Plzf , and Rorγt gene expression in mouse immune cells. • TQ-treated MSCs reduce TCF4 and Stat6 gene expression in mouse immune cells. • TQ induces MSC immunogenicity by influencing Plzf , Rorγt , and Tcf4 gene expression. [ABSTRACT FROM AUTHOR]