The clinical significance of extramedullary relapse (EMR) of acute myelogenous leukemia (AML) after allogeneic hematopoietic stem cell transplantation (allo-HSCT) remains poorly defined. Here we report the clinical outcomes of patients who underwent allo-HSCT for AML at our institution between 2000 and 2012. A total of 293 patients with AML who underwent allo-HSCT were included. The median duration of follow-up in survivors was 1840 days. Disease status at the time of allo-HSCT was complete remission in 192 patients and nonremission in 101 patients. A total of 110 patients experienced AML relapse after allo-HSCT, including 18 with EMR only, 83 with bone marrow relapse (BMR) only, and 9 with both EMR and BMR. The 5-year cumulative incidence of EMR after allo-HSCT was 9.5%, whereas that of BMR only was 28.9%. In multivariate analysis, peripheral blood stem cell transplantation was associated with an increased risk of EMR. The 2-year overall survival after post-transplantation relapse was 7.5% in patients with BMR only, 11.1% in those with both EMR and BMR, and 27.5% in those with EMR only (P < .05). Although the short-term survival was better in patients with EMR only, they rarely achieved long-term survival. Appropriate strategies for both post-transplantation EMR and BMR are needed.