Metabolic dysfunction in children is a major health issue. Pancreatic fat is a potential biomarker of metabolic dysfunction, but methodological difficulties have limited research on its role in at-risk children. This work used free-breathing abdominal MRI to quantify pancreatic fat and to characterize its heterogeneity in children with and without nonalcoholic fatty liver disease (NAFLD). Children with NAFLD had increased pancreatic fat that was heterogeneously distributed and predominantly located in the superior region. A simple region-of-interest-based measurement method failed to account for this heterogeneity, and thus underestimated pancreatic fat. Full segmentation pancreatic fat measurements correlated with markers of metabolic dysfunction.