The risk of cerebral infarction (CI) is contributed to the combination of environmental influences and genetic factors. The Apolipoprotein E (APOE) gene polymorphism as a risk factor in CI has been suggested, but direct evidence from genetic association studies remains inconclusive even in Chinese population. The purpose of this study was to identify association between the APOE ε2/ε3/ε4 polymorphism and the development of CI. Published relevant case-control studies were collected from electronic databases. Data were combined using odds ratio (OR) with 95% confidence interval (CI). Totally, 29 studies published from 1997 to 2012, involving 2,737 CI cases and 2,689 controls in Chinese population were subjected to final analysis. The pooled results suggested that CI subjects carrying ε4 allele had an increased risk for CI (ε4 vs. ε3: OR = 2.50, 95% CI 1.98-3.16, P < 0.001, ε4 carriers vs. E3E3 genotype: OR = 2.82, 95% CI 2.16-3.67, P < 0.001), compared with those carrying ε3 allele. However, carriers of APOE ε2 allele had no significant increased risk for CI, compared with those carrying ε3 allele. Potential publication bias was observed in the genetic model of ε4 versus ε3, but the results might not be affected deeply by the publication bias. Using the trim and fill method, the adjusted risk estimate for ε4 allele versus ε3 allele was attenuated but remained significant (OR = 2.00, 95% CI 1.59-2.53, P < 0.001), suggesting the stability of our results. Taken together, our study suggests that APOE ε4 allele is associated with an increased risk of developing CI in Chinese population.