This study aims to determine whether APOE alleles would affect the functional outcome in acute ischemic stroke (AIS) and whether the relationship between inflammation and stroke-related disability varies according to APOE genotypes. We retrospectively collected the demographic and clinical data of AIS patients within one week of symptom-onset through medical records review. The primary outcome was dependence or death, defined as modified Rankin scale (mRS) score of 2–6, which was assessed at 3 months. Among 1929 enrolled patients, the prevalence of APOE ε4 carriers was 17.73% (342/1929). There were 394 AIS patients (394/1929, 20.43%) showed poor function outcome of 90-day mRS (2–6), of whom 147 (147/342, 42.98%) were APOE ε4 carriers and 247 (247/1587, 15.56%) were non-ε4 carriers. There was a significant increased probability of poor functional outcome after AIS among APOE ε4 carriers versus non-ε4 carriers (adjusted-OR 4.62, 95% CI 3.51 to 6.09,
P
< 0.001). Among ε4 carriers, high neutrophil-to-lymphocyte ratio (NLR) was significantly associated with stroke-related disability (P
trend
= 0.035); however, no significant association was observed among non-ε4 carriers. Our study showed that the APOE ε4 carriers had worse functional outcome after AIS as compared with non-ε4 carriers. APOE genotype may modify the relationship between NLR and 3-month stroke outcome.