Objective To determine the correlations of the expression of T cell immunoglobulin domain and mucin domain-3 (TIM-3) on the surface of CD4+ T cells from peripheral blood with clinical stage and prognosis in the patients with non-small cell lung cancer (NSCLC). Methods A total of 69 patients with NSCLC were consecutively enrolled in this prospective study between September 2013 and September 2014 in Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, and 65 healthy people who underwent physical examination in the same period were enrolled as healthy controls. The expression of TIM-3 in peripheral blood was detected by flow cytometry. The NSCLC patients were divided into TIM-3 high-expression group and TIM-3 low-expression group by the median value of TIM-3 on peripheral CD4+ T cells. The relationships of TIM-3 expression with clinical features and prognosis were analyzed. Results The expression of TIM-3 on the CD4+ T cells in the NSCLC patients was significantly higher than that in the healthy controls (P < 0.05). High-expression of TIM-3 was significantly associated with lymph node metastasis and tumor stage (P < 0.05). Kaplan-Meier survival analysis showed that the patients with lower TIM-3 expression exhibited longer overall survival as compared to the patients with high TIM-3 expression (P < 0.05). Cox multivariate regression analysis showed that high expression of TIM-3 was an independent predictor for the overall survival in the patients with NSCLC (P < 0.05). Conclusions TIM-3 expression on CD4+ T cells is associated with clinical stage and overall survival in the NSCLC patients, and it may be a potential biomarker for predicting prognosis in the patients with NSCLC.