Background and aim Endoscopic ultrasonography is a reliable diagnostic modality for determining indications of endoscopic submucosal dissection for early gastric cancer. We aimed to clarify the clinical significance of endoscopic ultrasonography in the invasion depth diagnosis of early gastric cancer. Methods We retrospectively assessed 1598 consecutive patients with 2001 early gastric cancers who underwent EUS before ESD or surgery between October 2010 and April 2019 at our institution. Lesions were classified according to endoscopic ultrasonography-determined invasion depth as EUS-M/SM1 (lesions confined to sonographic layers 1 and 2 or lesions with changes in sonographic layer 3; depth, < 1 mm) and EUS-SM2 (lesions with changes in sonographic layer 3; depth, ≥ 1 mm). We evaluated the invasion depth determination accuracy of endoscopic ultrasonography and analyzed the clinicopathological features of misdiagnosed early gastric cancer cases. Results The invasion depth determination accuracy was as follows: EUS-M/SM1: pathological T1a/T1b1 early gastric cancer, 97%; EUS-SM2: pathological T1b2 early gastric cancer, 79%. The accuracy, sensitivity, specificity, positive predictive value, and negative predictive value were 95%, 98%, 69%, 97%, and 79%, respectively. In EUS-M/SM1 early gastric cancer, tumor size of ≥ 15 mm, presence of ulceration, and undifferentiated histological type were significantly associated with endoscopic ultrasonography accuracy. In EUS-SM2 early gastric cancer, tumor size of ≥ 30 mm was significantly associated with endoscopic ultrasonography accuracy. Conclusions Endoscopic ultrasonography is a useful modality in accurately determining the invasion depth of early gastric cancer before endoscopic submucosal dissection.