The detection rate of early-stage esophageal cancer has increased recently. Various types of treatment including endoscopic mucosal resection, blunt dissection, and esophagectomy with extended lymphadenectomy are employed in patients with submucosal esophageal cancer. The purpose of the present study was to analyze prognostic factors in patients with submucosal esophageal cancer. Univariate analysis showed that lymph node metastasis, subdivision of tumor depth, and lymphatic invasion were correlated with prognosis, whereas sex, age, tumor location, surgical procedure, adjuvant therapy, histologic findings, and venous invasion did not affect prognosis. Multivariate analysis demonstrated lymph node metastasis to be the only significant prognostic factor in submucosal esophageal cancer. Although subdivisions of tumor depth did not reach significance as prognostic factors, lymph node metastasis was strongly related to tumor depth. To select the individualized treatment in patients with submucosal esophageal cancer, accurate diagnosis of lymph node metastasis necessitates a combination of imaging methods such as endoscopic ultrasound-guided fine-needle aspiration, computed tomography, and positron emission tomography.