Hepcidin regulates iron metabolism. Its synthesis increases in infection and decreases in iron deficiency. The aim of this study was to evaluate the relationship between infection and iron deficiency by levels of hepcidin in children. A total of 350 school-age children participated in this cross-sectional study. Determinations of serum ferritin, hemoglobin, hepcidin, C-reactive protein, and α-1-acid-glycoprotein were done. Active infection was performed with a C-urea breath test. In schoolchildren without infection, hepcidin was lower in those with iron deficiency compared to children with normal iron status (5.5 ng/mL vs. 8.2 ng/mL, = 0.017); while in schoolchildren with infection the levels of hepcidin tended to be higher, regardless of the iron nutritional status. Using multivariate analysis, the association between infection and iron deficiency was different by hepcidin levels. The association between and iron deficiency was not significant for lower values of hepcidin (Odds Ratio = 0.17; 95% Confidence Interval CI 0.02-1.44), while the same association was significant for higher values of hepcidin (OR = 2.84; CI 95% 1.32-6.09). This joint effect is reflected in the adjusted probabilities for iron deficiency: Individuals with infection and higher levels of hepcidin had a probability of 0.24 (CI 95% 0.14-0.34) for iron deficiency, and this probability was 0.24 (CI 95% 0.14-0.33) in children without infection and lower levels of hepcidin. In children with infection and iron deficiency, the hepcidin synthesis is upregulated. The stimulus to the synthesis of hepcidin due to infection is greater than the iron deficiency stimulus.