Prior studies suggested that protein kinase Cη (PRKCH) 1425G/A polymorphism was associated with lacunar infarction. This study examined whether the association was independent of traditional risk factors in each of the stroke subtypes. This study included 206 ischemic stroke patients and 337 controls. Multivariable logistic regression was used for analyses. Co-variables of age, sex, hypertension, diabetes mellitus (DM), and smoking were included to delineate independency of associations. PRKCH 1425G/A was associated with ischemic stroke [odds ratio (OR) =1.5, 95% confidence interval (CI): 1.1-2.2, p = 0.024] when adjusted for age and sex. However, the significance of association became borderline when adjusted for co-variables (OR = 1.5, 95% CI: 1.004-2.3, p = 0.048). Of the infarction subtypes, PRKCH 1425G/A was associated with lacunar infarction (OR = 1.8, 95% CI: 1.1-2.9, p = 0.025), which remained significant when adjusted for co-variables (OR = 2.0, 95% CI: 1.1-3.5, p = 0.015). No association was found between the polymorphism and the other infarction subtypes. When stratified by age group, the magnitude of significance became stronger in patients >65 years old. Specifically, PRKCH 1425G/A was significantly associated with ischemic stroke in patients older than 65 years, when adjusted for all co-variables (OR = 2.0, 95% CI: 1.05-3.8, p = 0.036). Still, in patients older than 65 years, the association was only observed in lacunar infarction when adjusted for all co-variables (OR = 4.2, 95% CI: 1.7-10, p = 0.001). No association of PRKCH 1425G/A with stroke and any of the subtypes was identified in patients >65 years old. The association between PRKCH 1425G/A and lacunar infarction was independent of traditional stroke risk factors. PRKCH 1425G/A in stroke susceptibility differed between infarction subtypes and age groups.