Purpose To determine the prevalence of anemia and its association with Helicobacter pylori infection among adult dyspeptic patients. Patients and Methods A cross-sectional study was conducted among 283 dyspeptic patients at Kiryandongo General Hospital, in Uganda. A structured questionnaire was administered to capture demographic and clinical characteristics of study participants. Four milliliters of blood were then collected into an EDTA vacutainer for Complete Blood Count (CBC) and analyzed using HUMA COUNT 30 TS , and peripheral blood smears were made and stained using Giemsa stain. Anemia was defined as hemoglobin levels <12g/dl in females and <13g/dl in men according to the World Health Organization (WHO). Helicobacter pylori (H. pylori) stool antigen test was performed using Whole power H. pylori Ag rapid test device, and saline stool preparation was examined for intestinal parasites. Chi-squared test and Logistic regression were performed to determine association, and a p-value of ≤0.05 was considered statistically significant. Results The overall prevalence of Helicobacter pylori infection was 42.4% (120/283). The prevalence of anemia among H. pylori -infected patients was 25.8% (31/120) and 15.3% (25/163) among H. pylori -negative counterparts. H. pylori infection was significantly associated with anemia (p-value 0.042), age (p-value 0.02, 0.009), water sources (p-value 0.0049,) and intestinal parasitic infestation (p-value 0.02), respectively. Conclusion This study has shown that the prevalence of H. pylori infection and anemia is high among dyspeptic patients at Kiryandongo General Hospital. H. pylori infection was found associated with anemia, age, water sources, and intestinal parasitic infestation. Routine screening of anemia in H. pylori -infected individuals and further studies to explore the relationship between anemia and H. pylori disease is highly recommended.