Nutritional and dietary interventions are important in the prevention of stroke, but many of the factors influencing stroke remain undefined. Although omega-3/6 polyunsaturated fatty acids (PUFAs) have been suggested to be associated with cerebrovascular diseases, studies on this topic are lacking. This study extracted and screened independent single nucleotide polymorphisms of omega-3/6 PUFAs and 3 types of cerebrovascular diseases data from the IEU Open GWAS database. A two-sample Mendelian randomization (MR) was used to examine the association between omega-3/6 PUFAs with subarachnoid hemorrhage (SAH), intracerebral hemorrhage (ICH), and ischemic stroke (IS). The primary analysis method was the inverse variance weighting method, supplemented by the weighted median and MR-Egger methods. Sensitivity and multiplicity were assessed using Cochran Q test, MR-PRESSO, MR-Egger regression, and leave-one-out analysis. This study was conducted in full compliance with the STROBE guidelines throughout. The inverse variance weighting analysis revealed a negative correlation between omega-3 PUFAs and SAH (P = .0078). However, there was no correlation between omega-3 PUFAs and ICH (P = .3930) and IS (P = .2922). Additionally, there was no association between omega-6 PUFAs and SAH (P = .1399), ICH (P = .1399, 0.0660), and IS (P = .8571) using all 3 analytical methods. No heterogeneity or horizontal pleiotropy was observed. The study suggested that omega-3 PUFAs had a significant protective role in SAH. However, omega-3/6 PUFAs were not found to be associated with other types of cerebrovascular diseases.