Epithelial growth factor receptor (EGFR) mutations are present in 10%-26% of non-small cell lung cancer (NSCLC) tumors and are associated with the response to tyrosine kinase inhibitors (TKIs). This study aimed to detect and quantify the presence of circulating tumor cells (CTCs) in EGFR-mutant NSCLC patients and investigate their possible role in providing prognostic information. Enrolled patients received erlotinib (150 mg) or gefitinib (250 mg) orally once daily as the first-line treatment. Serial blood samples were taken at baseline (CTC-d0) and on day 28 (CTC-d28) following the initiation of erlotinib/gefitinib for detection of CTCs using the CellSearch system. CTCs ≥2 were found in 47/107 (44%) and CTCs ≥5 in 17/107 (15%). The CTC measurements were dichotomized as favorable (<5 CTCs) and unfavorable (≥5 CTCs) groups. The median progression-free survival (PFS) interval for patients in the favorable group at baseline was 11.1 months, significantly longer than the median PFS time of 6.8 months achieved by patients in the unfavorable group (p = 0.009). Patients in the favorable group on day 28 exhibited significantly longer PFS compared with patients in the unfavorable group (11.6 vs. 6.3 months; p < 0.0001). In univariate analysis, CTC-d0 ≥ 5 versus CTC-d0 = 0-4 was significantly associated with poor PFS and time-to-treatment failure (TTF). CTC-d28 ≥ 5 versus CTC-d28 = 0-4 was significantly associated with a poor PFS outcome. CTC-d0 and CTC-d28 remained independent poor prognostic markers in the stepwise multivariate analysis. Our study indicates that the CTC count is a prognostic factor for PFS and TTF outcomes in patients with advanced EGFR-mutant NSCLC.