Background: Fenestrations are rare, but well-known, vascular variations of the cerebral arteries. They are mostly incidental, asymptomatic angiographic findings and might precipitate vascular lesions such as AVM, aneurysmal dilatation, or even ischemic symptoms. However, association between arterial fenestration and brain aneurysms has not been clearly established. Objective: To evaluate whether incidence of arterial fenestrations are associated with brain aneurysm development and investigate the prevalence and most-common localizations of arterial fenestrations of the human brain. Design: Case–control study. Setting: All patients examined by CT angiography in University Hospital No. 4 in Lublin from 2009 to 2019. Patients: Each patient showing at least one cerebral aneurysm was included in the case group and each patient without cerebral aneurysm on CT angiography was included in the control group. Measurements: CT angiography examinations were conducted using the standard protocol used in the 1st Department of Radiology, Medical University of Lublin, Poland. The database and statistical research were conducted by use of the Statistica software (ver. 13.3, Tibco Software Inc., Palo Alto, CA, USA). Results: A total of 6545 CTA examinations were included in the study. Most of the aneurysms were located on the MCA: 629 (38.59%), ICA: 466 (28.59%) and AComA: 192 (11.78%). Cerebral arterial fenestration showed a non-statistically significant elevated risk for brain aneurysms in the entire study population (OR: 1.157; 95% CI: 0.826–1.621; p = 0.39). Among 6545 cranial CTA examinations, cerebral vessel fenestration was found in 49 of them, which constituted 0.75%. The most common vascular fenestrations were those located in the ACA (30.61%), BA (30.61%) and AComA (22.45%), while other fenestrations occurred infrequently. There were no significant differences in the age of patients in the individuals with vascular fenestration (p > 0.05). VA fenestration was slightly more common in men (16.67%) than in women (5.41%). However, these differences were not statistically significant (p = 0.216). Limitations: Our study has several limitations, including selection bias regarding examined population. Second, we assume that the total number of fenestrations detected in our study was underestimated due to the limitations of the CT method in comparison to other radiologic modalities. Conclusions: Cerebral arterial fenestrations are rare vascular malformations. The ACA is the most common localization of fenestrations, followed by BA and AComA. Fenestrations of cerebral arteries insignificantly increase the risk of cerebral aneurysm formation. Further prospective studies are necessary to make this association more precise.