Background: In recent years, cardiac progenitor cells (CPCs) are considered as a potential source of cell therapy for the treatment of heart failure. Despite the encouraging results of clinical trials showing that transplantation of CPCs improves function of infarcted hearts, reduced cell survival and inefficient engraftment into host tissue are still challenging issues. Methods: CPCs were isolated from a male mouse heart and incubated with estrogen (10-7M for 48 hours) in vitro. The heart failure model was generated by intraperitoneally isoproterenol (ISO) treatment (200mg/kg for 6 days) in the female mouse. Either estrogen pretreated-CPC (E2-CPC) or untreated-CPCs (Control-CPC) were intramyocardially transplanted into the failure heart. Engraftment of transplanted cells were visualized by in vivo imaging, Y-chromosome staining (by Fluorescence In Situ Hybridization) and SRY gene for expression analysis. Cardiac functions were determined by analyzing electrophysiological changes. Pathological changes following the transplantation were also examined at the molecular level by immunostaining and western blotting from isolated heart samples and on heart tissue sections to address the efficiency of the E2-CPC transplantation. In addition to regenerative outcomes at animal level, the enhancing effect of estrogen on the therapeutic potential of CPC was examined through changes in migration, proliferation and mitochondrial energetics by in vitro experiments. The effects of estrogen in transcriptome profiling was also evaluated by RNA sequencing (RNA-seq) in CPCs. Results: In vivo results demonstrated that estrogen pretreatment increased the retention rate of transplanted CPCs in failing heart. E2-CPC transplantation enhanced cardiac function and ameliorated pathological cardiac remodelling via inducing revascularization, proliferation while attenuating collagen formation and hypertrophy in failing heart. Our in vitro results have shown that estrogen treatment promotes migration, angiogenesis and proliferation capacities and adenosine triphosphate (ATP) production of CPCs in vitro. RNA sequencing provided further evidence that the change in the transcriptome profile of CPCs upon estrogen treatment improved their ability to cause reverse cardiac remodelling in the failing heart after transplantation. Conclusion: Our data indicated that estrogen-pretreatment significantly improves cardiac recovery in a failing heart through enhancing efficacy of CPC transplantation. This study also emphasized underyling mechanisms of the improvement in function in CPC-based therapies which remain poorly understood.