Background: Esophageal cancer (EC) and gastric cancer (GC) are common cancers and leading causes of cancer deaths worldwide. Many studies have investigated the association between dietary flavonols intake and the risk of EC and GC, but the results are inconsistent. Hence, we conducted a systematic analysis of relevant population-based studies to assess the association and derive a more precise estimation. Methods: The Cochrane, PubMed and Embase databases were searched to identify articles published through January 2016 that met the predetermined inclusion criterion. Twelve studies involving 4593 patients and 519,378 controls were included. Results: The summary odds ratios (ORs) of EC, GC and the two combined were respectively 0.88 (95% CI: 0.73–1.08), 0.80 (95% CI: 0.70–0.91) and 0.83 (95% CI: 0.74–0.92) for the highest category of dietary flavonols intake compared with the lowest. No significant heterogeneities were observed in these studies. Further analysis showed that the pooled ORs of EC and GC for cohort, population-based case-control and hospital-based case-control studies were 0.90 (95% CI: 0.61–1.34), 0.92 (95% CI: 0.72–1.18), 0.68 (95% CI: 0.38–1.24) and 0.83 (95% CI: 0.65–1.06), 0.84 (95% CI: 0.45–1.59), 0.70 (95% CI: 0.56–0.88). The subgroup analyses revealed a significant association of flavonol intake with a reduced risk of noncardia gastric adenocarcinoma but not gastric cardia adenocarcinoma. Moreover, significant inverse associations of flavonol intake with GC risk were observed in women but not in men, in smokers but not in nonsmokers, in European populations but not in American populations. Similarly, a significant inverse association of flavonols intake with EC risk was also observed in smokers but not in nonsmokers. Conclusion: High intake of dietary flavonols is significantly related to a reduced risk of GC, especially in women and smokers.