Although acute graft-versus-host disease (aGVHD) and chronic GVHD (cGVHD) are known causes of morbidity and mortality after allogeneic hematopoietic cell transplantation (HCT), the syndrome of late aGVHD is less well understood, particularly in children. We aimed to characterize the clinical features and response to therapy of late aGVHD and cGVHD by retrospectively reviewing 573 consecutive patients age <18 years who underwent their first allogeneic HCT at the University of Minnesota. We included patients with de novo late aGVHD (ie, first occurrence of aGVHD after day +100 post-HCT) and cGVHD. We retrospectively scored cGVHD cases based on the 2014 National Institutes of Health guidelines. At 3 years, 9 patients (2%) had developed late aGVHD, 16 (3%) had overlap cGVHD, and 7 had (1%) classic cGVHD. No cases of joint or genital cGVHD were observed. The overall response to therapy at 6 months was 78% (95% confidence interval [CI], 40% to 97%) after late aGVHD and 43% (95% CI, 23% to 66%) after cGVHD. Higher nonrelapse mortality from day +100 was seen in patients with cGVHD but not in those with late aGVHD compared with patients without GVHD (hazard ratio, 3.6 [95% CI, 1.3 to 10.0] and 1.6 [95% CI, 0.2 to 11.7], respectively). We found variable organ involvement and treatment responses between patients with late aGVHD and those with cGVHD in a single-center pediatric cohort. Further research is needed to investigate the risks and clinical features of late aGVHD and cGVHD in larger cohorts to better understand how to tailor even more effective GVHD preventive and therapeutic approaches in children.