Sugar-sweetened beverage (SSB) consumption has been associated with visceral fat partitioning in adults; however, the underlying mechanisms in childhood remain unclear and warrant exploration. This cross-sectional study aimed to investigate the association between SSB consumption and body fat in children aged 9–13 years and the potential modifying effect of children’s sex and serum cortisol levels. A sample of 2665 Greek schoolchildren participated in the ‘Healthy Growth Study’, and anthropometric, body composition, dietary intake and serum cortisol data were assessed. SSB consumption was defined as low (<1 serving/d), medium (1–2 servings/d) or high (>2 servings/d). We used linear regression models to assess the association between SSB consumption and measures of adiposity and to assess effect modification; models were stratified by sex and tertiles of morning serum cortisol. A significant positive association was observed between high SSB consumption and visceral adipose tissue (VAT) (β = 1·4, 95 % CI 0·4, 2·3, P = 0·01) but not BMI or BMI z-score. When stratified by sex, the association was observed in boys (β = 1·8, 95 % CI 0·3, 3·4, P = 0·02) but not in girls. When stratified by cortisol levels, SSB consumption was associated with VAT in children with cortisol levels in the lowest tertile (β = 2·8, 95 % CI 1·0, 4·6, P < 0·01). These results indicate that increased SSB consumption is associated with visceral adiposity in schoolchildren and this association may be modified by sex and morning serum cortisol. To prevent VAT accumulation and concomitant disease risk, dietary interventions should target SSB consumption during childhood.