This study aims to assess the efficacy of second allogeneic hemopoietic stem cell transplantation (allo-HSCT) for treating hemophagocytic syndrome with first engraftment failure. Among a total of 35 patients who underwent allo-HSCT between June 2015 and July 2021 for HLH, 10 patients who underwent a second HSCT following graft rejection were retrospectively analyzed. Various factors, such as the treatment course and outcome, the remission status, donor selection, and the conditioning regimen of patients before second allo-HSCT, were scrutinized for transplant-related complications and transplant-related mortality, as well as transplant outcomes. All the subjects have achieved complete donor engraftment, in which the neutrophils and platelets engraftment occurred in a median time of 12 d (range 10–19 d) and 24 d (range 11–97 d), respectively. Among the selected subjects, 20% of patients are diseased due to transplant-related thrombotic microangiopathy. Further, 90% of patients are diagnosed with aGVHD, in which 3 of them with grade I aGVHD, one patient with grade II aGVHD, two patients with grade III GVHD, and three patients with localized chronic GVHD. Moreover, 70% of patients showed signs of combined viral infections. Despite the complex symptoms, the overall survival rate is around 80%, with transplant-related mortality and the incidence of post-transplant GVHD of 20% and 60%, respectively. Together, our findings indicated that the second allo-HSCT showed great potential in treating hemophagocytic syndrome with engraftment failure.