We prospectively investigated the outcome of personalized second-line treatment based on epidermal growth factor receptor (EGFR) gene status in previously treated patients with advanced non-small cell lung cancer (NSCLC). EGFR gene status was evaluable by LH-mobility shift assay in registered patients. Gefitinib (Gef) treatment was recommended if the patients had EGFR mutation (mEGFR). EGFR gene status was evaluable in 146 patients. Seventy-four of the patients were female, 82 were smokers, and 122 had adenocarcinoma. Overall, 67 patients had mEGFR and received Gef. Forty-nine of 79 patients with wild-type EGFR (wEGFR) received other chemotherapies or radiation but 30 selected best supportive care only as a second-line treatment. Patients with mEGFR survived significantly longer than patients with wEGFR (p < 0.0001). However, the survival of patients who received other forms of chemotherapy was not different from that of patients who received best supportive care only as a second-line treatment in patients with wEGFR. Examination of the association between overall survival after first-line chemotherapy and prognostic factors using multivariate regression analysis showed that mEGFR and response to first-line chemotherapy were independent factors (p = 0.003 and p = 0.003, respectively). Selection of second-line treatment according to EGFR gene status may be useful for patients with NSCLC.