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). However, the impact of rEO-ED on brain morphometry remains largely unknown. Here we performed the largest magnetic resonance imaging-derived brain features comparison of children and early adolescents (<13 years) with EO-AN (n = 124) or ARFID (n = 50) versus typically developing individuals (TD, n = 116). EO-AN was associated with widespread cortex thinning, while underweight patients with ARFID exhibited reduced surface area and volumes compared with TD. Despite similar body mass index distributions, EO-AN and ARFID showed distinct structural patterns, suggesting independent brain mechanisms. Finally, we identified overlapping patterns of brain thickness differences between EO-AN and obsessive–compulsive disorder and between ARFID and autism spectrum disorder. Future studies are required to partition the contribution of body mass index versus rEO-ED mechanisms, as well as to identify shared mechanisms with other neurodevelopmental conditions toward a multidimensional approach of eating disorders.