The traditional Japanese dietary pattern, characterized by extremely low fat intake (<15% of energy), has long been regarded as a paradigm of healthy eating. Paradoxically, Japan remains one of the developed countries with the highest gastric cancer incidence globally. Current explanations focusing on high salt intake and Helicobacter pylori infection fail to fully account for this elevated risk. We propose a novel hypothesis: long-term extreme low-fat diet is an independent synergistic risk factor for gastric diseases in Japan. Chronic inadequate dietary fat intake impairs gastrointestinal mucosal barrier integrity through multiple mechanisms—reduced phospholipid synthesis, diminished prostaglandin E2 production, and disrupted gut microbiota homeostasis. This compromised mucosal barrier creates a "vulnerable state" that amplifies the damaging effects of established risk factors such as high salt consumption and H. pylori infection. Supporting evidence includes: (1) animal studies demonstrating that essential fatty acid deficiency impairs gastric mucosal protection and increases susceptibility to injury; (2) the Japan Collaborative Cohort Study showing that a western-style breakfast pattern, characterized by higher fat intake, was significantly associated with lower stomach cancer risk in males (HR 0.49, 95% CI 0.35–0.70) compared with a traditional Japanese-style breakfast; (3) temporal trends showing that increased fat consumption in Japan over 50 years correlates inversely with declining gastric cancer mortality, though concurrent lifestyle changes preclude causal attribution. This hypothesis provides a mechanistic explanation for the Japanese diet paradox and suggests that dietary fat optimization (20–30% of energy) should be considered as a complementary gastric cancer prevention strategy.