Helicobacter pylori (H. pylori) is one of the most common bacterial stomach infections and is implicated in a majority of non-cardia gastric cancer. While gastric cancer has decreased in the United States (US), the incidence in the Navajo Nation is nearly four times higher than surrounding Non-Hispanic White populations. Little is known about H. pylori prevalence in this population or other Indigenous communities in the lower 48 states. In this cross-sectional study, 101 adults representing 73 households from three Navajo Nation chapter communities completed surveys and a urea breath test for active H. pylori. Accounting for intrahousehold correlation, H. pylori prevalence was 56.4% (95% CI, 45.4–66.8) and 72% of households had at least one infected person. The odds of having an active infection in households using unregulated water were 8.85 (95% CI, 1.50–53.38) that of the use of regulated water, and males had 3.26 (95% CI, 1.05–10.07) higher odds than female. The prevalence of H. pylori in Navajo is similar to that seen in Alaska Natives. Further investigation into factors associated with prevention of infection is needed as well as understanding barriers to screening and treatment.