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The effect of body mass index (BMI) on esophageal and gastric carcinogenesis might be heterogeneous, depending on subtype or subsite. However, findings from prospective evaluations of BMI associated with these cancers among Asian populations have been inconsistent and limited, especially for esophageal adenocarcinoma and gastric cardia cancer. We performed a pooled analysis of 10 population‐based cohort studies to examine this association in 394,247 Japanese individuals. We used Cox proportional hazards regression to estimate study‐specific hazard ratios (HRs) and 95% confidence intervals (CIs), then pooled these estimates to calculate summary HRs with a random effects model. During 5,750,107 person‐years of follow‐up, 1569 esophageal cancer (1038 squamous cell carcinoma and 86 adenocarcinoma) and 11,095 gastric (728 cardia and 5620 noncardia) cancer incident cases were identified. An inverse association was observed between BMI and esophageal squamous cell carcinoma (HR per 5‐kg/m2 increase 0.57, 95% CI 0.50–0.65), whereas a positive association was seen in gastric cardia cancer (HR 1.15, 95% CI 1.00–1.32). A nonsignificant and significant positive association for overweight or obese (BMI ≥25 kg/m2) relative to BMI <25 kg/m2 was observed with esophageal adenocarcinoma (HR 1.32, 95% CI 0.80–2.17) and gastric cardia cancer (HR 1.24, 95% CI 1.05–1.46), respectively. No clear association with BMI was found for gastric noncardia cancer. This prospective study—the largest in an Asian country—provides a comprehensive quantitative estimate of the association of BMI with upper gastrointestinal cancer and confirms the subtype‐ or subsite‐specific carcinogenic impact of BMI in a Japanese population. The impact of BMI on upper gastrointestinal cancer by subtype or subsite among Asians is inconclusive. Using data from 10 large‐scale population‐based cohort studies, we evaluated the association between BMI and upper gastrointestinal cancers for 394,247 Japanese individuals. With 1038 esophageal squamous cell carcinoma, 86 esophageal adenocarcinoma, 728 gastric cardia cancer, and 5620 gastric noncardia cancer cases, we confirmed the subtype‐ or subsite‐specific carcinogenic impact of BMI in an Asian population.