Background: CYP4V2 polymorphisms were related to with venous thromboembolism. However, it is unclear on the influence of CYP4V2 polymorphisms on the susceptibility of ischemic stroke (IS). Methods: We selected and genotyped five polymorphisms in CYP4V2 to test whether CYP4V2 variants confer to the risk for IS in a Chinese Han population with 575 cases and 575 controls. Genotyping of CYP4V2 polymorphisms was performed using the Agena MassARRAY platform. Logistic regression analysis was used for the association by calculating odds ratios (ORs) and 95% confidence interval (CI). False-positive report probability (FPRP) analysis was applied to assess the noteworthy relationship of the significant findings. Results: Rs1398007 might be a risk factor for IS occurrence (OR = 1.34, 95% CI: 1.05–1.71, p = 0.009). Specially, confounding factors (age, gender, smoking and drinking status) might contribute to the relationship of rs1398007 with IS susceptibility. Moreover, rs1053094 and rs56413992 were associated with IS risk in the male population. Multifactor dimension reduction (MDR) analysis showed a combination of rs13146272 and rs3736455 with the strongest interaction effect (information gain values of 0.40%). Furthermore, the genotypes of rs1398007 (p = 0.006) and rs1053094 (p = 0.044) were associated with the levels of HDL-C among healthy controls. Conclusions: Our results firstly provided evidence that CYP4V2 rs1398007 might be a risk factor for IS occurrence, which might provide instructive clues for CYP4V2 to the pathogenesis of IS.