We aimed to find out predictive markers for lymph node (LN) metastasis of early gastric carcinoma (EGC) by separating evaluation of protein expression in mucosa and submucosa considering tumor heterogeneity. We selected 37 pN1–3 EGCs and depth- and size-matched 31 pN0 EGCs as training set and 72 EGCs including 14 pN1–3 EGCs as test set. Protein expression for β-catenin, E-cadherin, N-cadherin, galectin-3, c-MET, TrkB, and Ki-67 was assessed by immunohistochemistry in mucosal (-m) and submucosal (-sm) portions of tumor. In the training set, Ki67-m was higher than in Ki67-sm (mean ± SD: 82.67 ± 11.99% vs 61.79 ± 22.53%, p < 0.001). Altered E-cadherin-sm, high Ki67-m, and high Ki67-sm were correlated with LN metastasis (p < 0.05) and Ki67-sm was independent with lymphatic invasion and desmoplasia (p = 0.015 by multivariate logistic analysis). The test set confirmed Ki67-sm and E-cadherin-sm as predictors of LN metastasis (p < 0.05). Submucosal EGCs with ≥2 predictive factors out of high Ki67-sm, altered E-cadherin-sm, large tumor size (≥3 cm), diffuse type histology, and present lymphatic invasion yielded 100% sensitivity and 90.9% specificity for prediction of LN metastasis in 21 submucosal EGCs of test set. The proliferative activity of tumor in submucosa is suggested to be an independent predictor for LN metastasis in EGC.