Acute myeloid leukemia (AML) in first remission (CR1) with isolated NPM1 mutation (iNPM1m) is considered a good prognosis genotype, although up to one-third relapse. To evaluate the best transplant strategy, we retrospectively compared autologous stem cell transplantation (auto-SCT), related (MSD), and fully matched unrelated (MUD) allogeneic stem cell transplantation (allo-SCT). We identified 256 adult patients including 125 auto-SCT, 72 MSD, and 59 MUD.The 2-year leukemia-free survival (LFS) was 62% in auto-SCT, 69% in MUD, and 81% in MSD (P = .02 for MSD vs others). The 2-year overall survival (OS) was not different among auto-SCT, MUD, and MSD, reaching 83% (P = .88). The 2-year non-relapse mortality (NRM) was 2.5% in auto-SCT and 7.5% in allo-SCT (P = .04). The 2-year cumulative incidence of relapse (RI) was higher after auto-SCT (30%) than after MUD (22%) and MSD (12%, P = .01). In multivariate analysis, MSD versus auto-SCT but not MUD versus auto-SCT was associated with lower RI (P < .01 Mohamad Mohty, Jordi Esteve, and Arnon Nagler contributed equally to this study.