This study aimed to clarify the potentiality of bone marrow mesenchymal stem cells (BM-MSC) transplantation with albendazole (ABZ) on the modulation of immune responses against hydatid cyst antigens and the regeneration of injured livers in experimentally infected rats. Three different antigens of hydatid cyst fluid (HCF), hydatid cyst protoscolex (HCP) and hydatid cyst germinal layer (HCG) were isolated and their antigenic potencies were determined. The ultrasound, immunological and pathological criteria were investigated. Counting of 80% confluence BM-MSC was 4.68 × 104 cells/cm2 with 92.24% viability. Final population doublings score was 65.31 that indicated proliferation and self-renewability. Phenotyping of BM-MSC showed expression of CD73 and CD29 without exhibition of CD34 and CD14. Ultrasound examination showed multiple hydatid cysts in liver with low blood flow and spleenomegaly 8 weeks’ post infection. No significant differences were noted in cystic diameter in uni-cyst liver at 2nd and 4th weeks following ABZ treatment while it was significantly decreased (P < 0.05) following transplantation of BM-MSC + ABZ treatment comparing to experimentally infected untreated group. Igs and IgG responses to the three antigens were significantly elevated while elevation in IgM response was only to HCG (P < 0.05). ABZ treatment accompanied with significant decrease in Igs and IgG titers against HCF and HCG only at 4th week post treatment (P < 0.05). However, Igs titer against HCF, HCP and HCG was significantly decreased at the 4th week following transplantation of BM-MSC + ABZ. Interestingly, the combination of BM-MSC + ABZ treatment resulted in reduction of Igs response to HCP to normal level as that of healthy control. Experimental infection resulted in elevation of TNF-α and IL-6 (P < 0.05) while, IL-4 and IL-10 decreased (P < 0.01). After transplantation of BM-MSC + ABZ treatment, serum TNF-α and IL-6 concentrations were reduced (P < 0.05) at both the 2nd and 4th weeks. However, IL-4 and IL-10 concentrations were significantly elevated (P < 0.05) only at 4th week following transplantation of BM-MSC + ABZ treatment. In conclusion, BM-MSC transplantation following ABZ administration can regenerate injured liver tissue without complete disappearance of hydatid cyst. In addition, it can modulate host protective humeral and cell mediated immune responses against hydatid cyst antigens. Therefore, the current study encourages to move to the step of performing clinical trials in humans.