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Tissue biopsy is often not very accurate for the diagnosis of gastric epithelial neoplasia (GEN), and the results differ notably from endoscopic resection (ER) in terms of the pathological diagnosis. The aims of this study were to evaluate the diagnostic performances of biopsy, magnifying endoscopy with narrow-band imaging (ME-NBI), and biopsy plus ME-NBI for GEN. This study retrospectively analyzed 101 cases diagnosed as GEN using ER samples. The discrepancies between biopsy and ER, as well as between biopsy plus ME-NBI and ER in the diagnosis of GEN were evaluated. Factors that contributed to such discrepancies were analyzed. The sensitivity and specificity of biopsy and ME-NBI for the diagnosis of high-grade neoplasia (HGN) were determined. The discrepancy in the pathological diagnosis between biopsy and ER was 39.6% for GEN and 54.2% for HGN. The discrepancy between biopsy combined with ME-NBI and ER was 15.9% for GEN and 10.2% for HGN. Factors that undermined the diagnostic accuracy of biopsy included the lesion size (≤10 mm, odds ratio [OR] 1; 10–20 mm, OR 0.2, 95% confidence interval [CI] 0.1–0.7; >20 mm, OR 0.5, 95% CI 0.1–2.1, P = 0.03) and the number of biopsy fragments (OR 0.6, 95% CI 0.5–0.8, P = 0.001). The sensitivity and specificity for HGN were 45.8% (33.7%–58.3%) and 100% (87.5%–100%) for biopsy, and 88.1% (77.5%–94.1%) and 92.9% (81.0%–97.5%) for ME-NBI, respectively. In conclusion, biopsy-based diagnoses for GEN should be interpreted with caution. Biopsy combined with ME-NBI can contribute to the diagnosis of GEN, which improves diagnostic consistency with pathological result of ER specimens.