Background Clinical staging of gastric cancer (GC) before treatment is essential. Endoscopic ultrasound (EUS) is a recommended staging tool, but its efficacy remains controversial. Our previous prospective study evaluated the potential value of EUS for T staging and presented discrepancies. In this study, we aimed to evaluate the efficacy of EUS in T staging by comparing it with pathological staging. We analyze the factors that can potentially affect accuracy to identify suitable subgroups for EUS staging.Methods Data from a total of 1763 consecutive patients with GC from January 2015 to December 2017 were analyzed. Results from EUS and pathological T staging were compared. The factors that might affect EUS’s accuracy were analyzed.Results The sensitivity, specificity, positive predictive value, and negative predictive value of EUS in patients with early GC were 62.08%, 96.13%, 90.94%, and 80.21%, respectively. The accuracy rates of uT1, uT2–uT4, and uT3–uT4 were 90.94%, 79.02%, and 78.39%, respectively. In multivariate analysis, underestimation was more likely to be observed in patients with tumors located in the middle or upper third of the stomach. Overestimation was more likely to be observed in patients with tumors located in the lower third or those without ulcer. Other factors affecting accuracy included ulcer, differentiation, larger size and undergoing surgery.Conclusion Our findings highlight the role of EUS in determining the T staging of GC. Overestimation and underestimation in T-staging were significantly associated with the tumor location in early GC, and a decision-making algorithm was proposed for clinical practice in early cancers based on these findings.