We retrospectively analyzed the effect of conditioning intensity on 22 late complications in 145 adolescent and young adults who underwent allogeneic hematopoietic cell transplantation (HCT) in childhood. Seventy-six patients received myeloablative conditioning (MAC), while 69 received reduced-intensity conditioning (RIC). Incidence rates of late complications (≥ 1), organ dysfunction, endocrine/metabolic abnormalities, and psychosocial issues in evaluable patients were 71.0%, 17.2%, 66.2%, and 9.0%, respectively. The prevalence of short stature, impaired glucose tolerance, dyslipidemia, and gonadal dysfunction was significantly higher in the MAC group than in the RIC group. Multivariate analyses identified conditioning regimen as an independent factor for gonadal dysfunction and impaired glucose tolerance, but not for short stature. In contrast, inverse probability of treatment weighting analysis revealed that the prevalence of not only gonadal dysfunction and impaired glucose tolerance, but also of short stature, was significantly higher in the MAC group than in the RIC group. The prevalence of organ dysfunction, secondary malignancies, and psychological issues did not differ significantly between the two groups. Reducing conditioning intensity significantly influenced various endocrine complications but not organ dysfunction or psychosocial issues. These findings will inform selection of optimal conditioning regimens and development of practical long-term follow-up systems for pediatric HCT recipients.