We retrospectively studied patients who relapsed after allogeneic stem cell transplantation (SCT) to identify factors influencing outcomes. Of the 296 patients (196 with AML and 100 with ALL), 102 (34%) experienced relapse at a median of 222 days (range: 30-2,748) after SCT. Multivariable analysis showed that high disease risk (hazard risk [HR]: 1.95; 95% confidence interval [CI]: 1.17-3.24; p = 0.010), unrelated donor (HR: 1.76; 95% CI: 1.10-2.80; p = 0.018), and interval of < 180 days from SCT to relapse (HR: 2.10; 95% CI: 1.26-3.51; p = 0.004) were independent factors of 2-year post-relapse survival (PRS). These factors were used as a prognostic index for PRS. The 2-year PRS in patients of score 0, score 1, score 2, and score 3 was 38%, 19%, 3%, and 0%, respectively (p < 0.001). Our new prognostic index may be helpful for selecting the treatment for relapsed patients after SCT.