The expression of human epidermal growth factor receptor 2 (HER2) is related to tumor progression in many human malignancies. This study evaluated the significance of HER2 in early-stage non-small cell lung cancer (NSCLC). Specimens were obtained from 172 patients with early-stage (T1-T2N0M0) NSCLC, which included T1N0M0 (n = 52) and T2N0M0 (n = 120). The expression of HER2 was determined by immunohistochemistry (IHC). HER2 expression and its relationship with clinicopathological parameters and survival were analyzed. The expression of HER2 was significantly higher in the non-squamous cell carcinoma than in the squamous cell carcinoma (74.3 % vs. 53.7 %, p = 0.008). HER2 expression and tumor size were independent prognostic indicators in the multivariate analysis (p = 0.007 and p = 0.015, respectively). Expression of HER2 indicated a worse 5-year overall survival (65 % vs. 86 %, p = 0.014), especially for stages IB and IIA diseases (p = 0.035 and p = 0.043, respectively) and adenocarcinoma (p = 0.047). Therefore, HER2 may be related with the pathogenesis of NSCLC and act as an unfavorable prognostic factor in T1N0M0 and T2N0M0 NSCLC, especially in stages IB and IIA diseases.