Studies on the role of protein intake in the development of stomach cancer (SC) remain controversial. This study examines the relationship between protein intake from whole foods and SC in a Vietnamese population. A case-control study was designed in the university hospitals in Hanoi, Vietnam, from 2003 to 2019. Participants included 1182 SC cases and 2995 controls. Of the participants, 2,580 were men, and 1,597 were women. Protein intake was assessed using a validated semi-quantitative food frequency questionnaire. The odds ratio and 95% confidence interval (OR, 95%CI) examined the risk of SC associated with total protein and subgroups of mammal-animals and fish-poultry protein. Overall protein intake was negatively associated with SC (fifth vs. first quintile: OR (95%CI): 0.41 (0.32, 0.51). The dose-response relationship was also observed per increment quintile, OR (95%CI): 0.81 (0.77, 0.86) for both genders, OR (95%CI): 0.82 (0.77, 0.88) in men, OR (95%CI): 0.80 (0.73, 0.87) in women, OR (95%CI): 0.82 (0.77, 0.86) for noncardiac and OR (95%CI): 0.79 (0.63, 1.00) for cardiac stomach cancer. The beneficial effects of SC remained for the protein sources from mammal-animals and fish-poultry protein. The significant inverse association between protein intake remained in the ever and never tobacco smoking, no-alcohol use and alcohol use, blood group A and AB, and O, H. Pylori infected group, and the status of body-mass-index. The findings suggest that a high-protein diet is associated with lower SC risk. Further investigation is warranted to understand the beneficial effect of protein intake against stomach cancer.