We aimed to evaluate the impact of pre-transplant imatinib administration on the outcome of allogeneic hematopoietic stem cell transplantation (allo-HSCT) in adults with Philadelphia chromosome-positive (Ph+) acute lymphoblastic leukemia (ALL). We retrospectively analyzed 738 patients with Ph+ALL that underwent allo-HSCT between 1990 and 2010 using data from the Transplant Registry Unified Management Program of the Japan Society of Hematopoietic Cell Transplantation. We compared the allo-HSCT outcomes between 542 patients who received imatinib before allo-HSCT during the initial complete remission period (imatinib cohort) and 196 patients who did not receive imatinib (non-imatinib cohort). The 5-year overall survival after allo-HSCT was significantly higher in the imatinib cohort than in the non-imatinib cohort [59% vs. 38%; 95% confidence interval (CI), 31%-45%; P < 0.001]. Multivariate analysis indicated that pre-transplant imatinib administration had beneficial effects on overall survival [hazard ratio (HR), 0.57; 95% CI, 0.42-0.77; P < 0.001], relapse [HR, 0.66; 95% CI, 0.43-0.99; P = 0.048], and non-relapse mortality (HR, 0.55; 95% CI, 0.37-0.83; P = 0.005). In conclusion, our study showed that imatinib administration before allo-HSCT had advantageous effects on the clinical outcomes of allo-HSCT in patients with Ph+ALL.