Early-onset restrictive eating disorders (rEO-ED) encompass a heterogeneous group of conditions, including early-onset anorexia nervosa (EO-AN) and avoidant restrictive food intake disorders (ARFID). Almost nothing is known about the consequences of rEO-ED on brain development. We performed the largest comparison of MRI-derived brain features in children and early adolescents (<13 years) with EO-AN (n=124), ARFID (n=50), and typically developing individuals (TD, n=112). Despite similar body mass index (BMI) distributions, EO-AN and ARFID showed divergent structural patterns, suggesting independent brain mechanisms. Half the regional brain measures were correlated with BMI in EO-AN and none in ARFID, indicating a partial mediation of EO-AN signal by BMI. EO-AN was associated with a widespread pattern of thinner cortex, while underweight ARFID patients exhibited smaller surface area and subcortical volumes than TD. Future studies will be required to partition the contribution of low BMI vs. ED mechanisms in neurodevelopmental disorders.