Background <p>Multisite pain is common during adolescence and is influenced by sex-related neurobiological and developmental factors, but its developmental neural mechanisms are unclear.</p> Methods <p>Utilizing data from the Adolescent Brain and Cognitive Development Study, we investigated the relation between cortical brain structure and multisite pain (assessed by youth self-reports of painful regions on a body map) in male (<i>N</i> = 3,299) and female (<i>N</i> = 2,844) adolescents aged 11–12 years. We focused on brain regions functionally linked to multisite pain (i.e., bilateral sensorimotor, cingulate, fronto-insular and inferior parietal cortex). We also explored the moderating role of pubertal status (assessed by the Pubertal Development Scale).</p> Results <p>Findings revealed distinct brain structure-pain associations in male and female youth. Male youth exhibited an inverse linear relation between cortical thickness of the left pre- and postcentral gyri and number of pain sites. Female youth exhibited a non-linear relation between surface area of the right supramarginal gyrus and number of pain sites. Pubertal status moderated the cingulate cortical thickness-pain association in males; those in early puberty had an inverse relation between anterior and mid cingulate cortex thickness and pain sites, whereas this relation was positive in those beyond mid-puberty.</p> Conclusion <p>This study provides valuable insights into the sex-dependent neural organization linked to adolescent pain.</p>