Ultra-processed food (UPF) consumption impacts nutrient intake and plays an important role in non-communicable diseases (NCD), even among schoolchildren. This cross-sectional study aimed to characterize the food consumption of this population and its relationship with laboratory and anthropometric aspects. A sample of 190 subjects aged 5 to 19 y was randomly selected for dietary, laboratory, and anthropometric assessment. Statistical inference was calculated using Spearman’s correlation. Excess weight was observed in 34%, a high Waist-to-Height Ratio in 9%, and hypertriglyceridemia in 17% of the subjects, higher among those from urban schools (45%, p = 0.011; 15%, p = 0.015; 24%, p = 0.026, respectively). UPF consumption represented 21% of caloric intake and showed a positive correlation with trans fatty acids (r = 0.70) and sugar (r = 0.59) intake. Unprocessed food consumption showed a weak, but significant, correlation with Body Mass Index (r = 0.22) and Waist Circumference (r = 0.23), while processed meat showed a negative correlation with serum ferritin (r = −0.16) and vitamins D (r = −0.20) and B12 (r = −0.15). These findings highlight the need for public policies to promote Food and Nutritional Security for schoolchildren to prevent NCD and nutritional deficiencies.