Childhood obesity has been associated with increased sodium intake. Nonetheless, evidence linking sodium intake to Body Mass Index (BMI) and Body Fat Mass Percentage (%BF) remains limited, especially in the pediatric age group. Therefore, this study aims to investigate whether there is an association between 24 h urinary sodium excretion with BMI and %BF in a sample group of children from the ARIA study. This cross-sectional analysis included 303 children aged 7 to 12 from across 20 public schools in Porto, Portugal. Weight and %BF were assessed using the Tanita™ BC-418 Segmental Body Analyzer. Children’s Total Energy Intake (TEI) was estimated through a single 24 h Recall Questionnaire, and urinary sodium and potassium excretion was estimated by a 24 h urine collection. The association of %BF and BMI with 24 h sodium excretion was estimated by a binary logistic regression adjusted for sex, age, physical activity, total energy intake, parental education, and 24 h urinary excreted potassium. There was a significant positive association between higher levels of urinary sodium excretion and higher %BF values, even after adjusting for confounders. However, the same was not observed for BMI. Our findings suggest that higher sodium intake is associated with higher values of %BF among children, regardless of TEI and potassium intake.