Background: Ultra-processed food consumption and obesity have been highlighted as an important relationship to public health. We aimed to evaluate the association between ultra-processed food consumption and body fat from 6 to 11 years of age. Methods: We assessed the association between ultra-processed food consumption (from food frequency questionnaires) and body fat (measured by air displacement plethysmography) between 6 and 11 years of age among participants of the Pelotas-Brazil 2004 Birth Cohort. The NOVA classification was used to classify foods according to the processing degree. Body fat was evaluated relative to the height using fat mass index (FMI). Generalized estimating equations were used to answer the main research question and mediation analyses were run to assess the direct and indirect effect of ultra-processed food in body fat. Results: At fully adjusted analysis, an increase of 100 g in contribution from ultra-processed food to daily food intake at between 6 and 11 years of age was associated with a gain of 0.14 kg/m2 in FMI in the same period; 58% of the total effect of ultra-processed food intake at 6 years (in grams) over the change in FMI from 6 to 11 years was mediated by its calorie content. Conclusions: Ultra-processed food consumption was associated with an increase in body fat from childhood to early adolescence, and this association was not just due to the effect of ultra-processed food on calorie content.