The outcomes of allogeneic hematopoietic cell transplantation (HSCT) in patients with biphenotypic acute leukemia (BAL) remain unclear. We retrospectively analyzed the outcomes of HSCT in BAL patients in Japan in comparison to acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) using the registration data from a nationwide database. The data of 90, 5371, and 3301 patients with BAL, AML, and ALL, respectively, were included in the analysis. The median follow-up period was 1481.5 days (range: 0–5556). The 5-year overall survival (OS) of the BAL, AML, and ALL patients were 39.6, 41.8, and 42.0 %, respectively (BAL vs. AML, P = 0.98 BAL vs. ALL, P = 0.77). A multivariate analysis revealed that, in comparison to BAL, AML with a better-risk karyotype was associated with superior OS. An analysis of the prognostic factors of BAL patients showed that OS was significantly longer in patients who were in their first complete remission in comparison to patients who were not in remission. Our data suggest that HSCT is an effective treatment for BAL patients, regardless of the presence of any known poor prognostic factors other than a non-remission status.