Although cytogenetic abnormalities at diagnosis are recognized as an important prognostic factor in patients with Philadelphia chromosome (Ph)-negative acute lymphoblastic leukemia (ALL), the prognostic impact has not been evaluated in allogeneic stem cell transplant (allo-SCT) recipients. Thus, we assessed 373 Ph-negative ALL patients who underwent allo-SCT. The high-risk (HR) group included those with t(4;11), t(8;14), low hypodiploidy, and complex karyotype, and the standard risk (SR) group included all other karyotypes. Among the 204 patients who underwent a transplant during the first remission (167 in the SR group and 37 in the HR group), the overall survival (OS) rates were similar between these groups (64.1% vs. 80.0% at 5 years, respectively; p = 0.12). Conversely, among the 106 patients who underwent a transplant while not in remission (84 in the SR group and 22 in the HR group), patients in the SR group showed a significantly superior OS rate compared to the HR group (15.4% vs. 4.5% at 5 years, respectively; p = 0.022). These results suggested that treatment outcomes of Ph-negative ALL patients with HR cytogenetic abnormalities may improve following allo-SCT, especially in the first remission. Innovative transplant approaches are warranted in patients who are not in remission.