To investigate the associations of breastfeeding with overall and regional body composition at 11 years of age, and to assess whether ultra-processed food (UPF) consumption mediates these associations. This prospective cohort study included participants from the 2004 Pelotas Birth Cohort, Brazil. Breastfeeding data were collected in early childhood, and overall and regional body composition were assessed at 11 years of age. Multiple linear regression models were used to examine the associations of exclusive and total breastfeeding duration, as well as breastfeeding patterns at 3 and 12 months, with overall (BMI z-score, fat mass index [FMI], and fat-free mass index [FFMI]) and regional body composition (android fat mass [AFM], gynoid fat mass [GFM], and appendicular lean soft tissue [ALST]). Mediation analysis was performed using the G-computation formula, considering UPF consumption at 6 years of age. Associations between breastfeeding and body composition were sex-specific and varied according to the breastfeeding indicator. Among boys, longer exclusive breastfeeding was associated with lower AFM, whereas receiving any breast milk at 3 months and longer total breastfeeding duration were associated with higher BMI z-score, FFMI, and regional lean and gynoid mass. Among girls, longer exclusive breastfeeding was associated with higher BMI z-score, FMI, GFM, and ALST, while continued breastfeeding at 12 months was associated with higher BMI z-score, FMI, FFMI, GFM, and ALST. UPF consumption did not mediate the associations between breastfeeding and body composition. Breastfeeding was associated with body composition at 11 years of age, particularly with regional fat distribution and lean mass, although the direction and magnitude of associations differed by sex and breastfeeding indicator. The findings suggest that breastfeeding may influence not only adiposity but also fat distribution and lean mass development.