<b><i>Backgrounds:</i></b> Previous studies reported inconsistent results regarding associations between apolipoprotein E (<i>APOE</i>) polymorphism and clinical outcomes after ischemic stroke (IS), intracerebral hemorrhage (ICH), or subarachnoid hemorrhage (SAH). Thus, the study was designed to make a systematic review and meta-analysis regarding the association between <i>APOE</i> polymorphism and clinical outcome after IS, ICH, and SAH. <b><i>Methods:</i></b> To identify studies eligible for this meta-analysis, we searched for articles published before August 2021 in the databases (PubMed, Web of Science, and Google Scholar). We used STATA 12.0 software to compute hazard ratios (HRs) and their 95% confidence intervals (CIs) regarding <i>APOE</i> polymorphism and clinical outcome after IS, ICH, and SAH. <b><i>Results:</i></b> Meta-analysis showed no significant association between <i>APOE</i> polymorphism and functional outcome after IS with fixed effects models (ε4 carrier vs. non-ε4 carrier: HR, 1.00; 95% CI: 0.83–1.21, <i>I</i><sup>2</sup> = 29.4%, <i>p</i> = 0.183; ε2 carrier vs. non-ε2 carrier: HR, 0.92; 95% CI: 0.72–1.16, <i>I</i><sup>2</sup> = 15.6%, <i>p</i> = 0.307). Meta-analysis showed that ICH patients carrying ε4 allele have increased risk of poor outcome in Caucasian population with fixed effects models (ε4 carrier vs. non-ε4 carrier: HR, 1.75; 95% CI: 1.19–2.57, <i>I</i><sup>2</sup> = 0.0%, <i>p</i> = 0.543). Meta-analysis showed no significant association between <i>APOE</i> polymorphism and functional outcomes after SAH with random effects models (ε4 carrier vs. non-ε4 carrier: HR, 1.51; 95% CI: 0.80–2.84, <i>I</i><sup>2</sup> = 57.1%, <i>p</i> = 0.022). <b><i>Conclusions:</i></b> In conclusion, the present study demonstrated <i>APOE</i> ε4 carriers show worse functional outcomes after ICH, but not after IS or SAH. More large-scale studies were critical to explore the association between <i>APOE</i> polymorphism and clinical outcome after IS, ICH, and SAH.