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 H. pylori 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 H. pylori infection was performed with a 13C-urea breath test. In schoolchildren without H. pylori 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, p = 0.017); while in schoolchildren with H. pylori infection the levels of hepcidin tended to be higher, regardless of the iron nutritional status. Using multivariate analysis, the association between H. pylori infection and iron deficiency was different by hepcidin levels. The association between H. pylori 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 H. pylori 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 H. pylori infection and lower levels of hepcidin. In children with H. pylori infection and iron deficiency, the hepcidin synthesis is upregulated. The stimulus to the synthesis of hepcidin due to H. pylori infection is greater than the iron deficiency stimulus.