Observational and preclinical studies suggested an association between the expression of thymidylate synthase (TS) and clinical effects of pemetrexed-based chemotherapy in non-small-cell lung cancer (NSCLC) patients. However, the predictive value of TS for pemetrexed-containing chemotherapy regimen remained controversial. The aim of the study was to further appraise the association between the expression of TS and clinical efficacy pemetrexed-based chemotherapy in NSCLC patients. We searched in MEDLINE (PubMed), EMBASE, and Cochrane Library from January 1945 to May 2013. Two authors independently extracted information from the characteristics of study participants. Primary outcomes included therapeutic response (TR; i.e., complete response + partial response vs. stable disease + progressive disease), progression-free survival (PFS), and overall survival (OS). Relative risk (RR) and hazard ratio (HR) were used for evaluating the risk or hazard. Eight studies were included in the meta-analysis. Better response usually appeared in NSCLC patients with a lower expression of TS [RR = 2.06 95 % confidence intervals (CI) 1.44, 2.96]. There was a significant association between TS expression and outcomes of pemetrexed-based chemotherapy for NSCLC (PFS: HR = 0.63 95 % CI 0.52, 0.76; OS: HR = 0.74, 95 % CI: 0.63, 0.88). In addition, no evidence of publication bias was observed. This meta-analysis evaluated the predictive value of TS and provided evidence that NSCLC patients with lower TS expression could significantly benefit from pemetrexed-based chemotherapy. This increased level of TS was probably an independent risk factor of potential resistance against pemetrexed.