Clinical efficacy of allogeneic hematopoietic cell transplantation (HCT) using reduced-intensity conditioning (RIC) for younger patients remains unclear. We therefore performed a retrospective registry-based study to evaluate outcomes for patients with AML aged between 16 and 49 years who underwent RIC allogeneic HCT. Patients receiving RIC (N = 125) showed significantly worse survival than those receiving myeloablative conditioning (MAC; N = 1,554) (47.7% for RIC and 54.2% for MAC at 4 years, P = 0.047). However, the difference became marginal after adjustment for patient characteristics (P = 0.080), and inclusion in the multivariate analysis of the HCT comorbidity index or the propensity score for estimating the likelihood of choosing RIC or MAC further reduced statistical significance (P = 0.371 and 0.206, respectively), indicating the existence of a selection bias against RIC. Nevertheless, outcomes for our patients receiving RIC were still acceptable, so that RIC constitutes a potential therapeutic option for younger AML patients who are deemed unsuitable for MAC. Subgroup analyses showed that patients aged between 40 and 49 years as well as those in first or second CR at the time of transplantation exhibited similar outcomes regardless of whether they were treated with RIC or MAC.