Objective Arteriovenous fistulas (AVFs) at the cranio-cervical junction (CCJ) are uncommon conditions with complex angioarchitecture. The objective of this study was to identify the angioarchitectural features of CCJ-AVF to predict the risk of clinical presentation.Methods The study population was comprised of 68 consecutive patients with CCJ-AVF at two neurosurgical centers between 2014 and 2022, and a systematic pooled analysis of 68 cases with detailed clinical data obtained via PubMed database from 1990 to 2022. Clinical and imaging data were collected to analyze factors for subarachnoid hemorrhage (SAH), myelopathy, and modified Rankin scale (mRS) at presentation.Results The mean age of the patients was 54.5 ± 13.1 years, and 76.5% of patients were male. The most common feeding arteries was V3-medial branches(33.1%), and drainage was frequently through the anterior or posterior spinal vein/perimedullary vein (72.8%). The most common presentation was SAH(49.3%), and an associated aneurysm (adjusted OR, 7.44; 95%CI, 2.89–19.15) was a risk factor for SAH. Anterior or posterior spinal vein/perimedullary vein (adjusted OR, 2.78; 95%CI, 1.00-7.72) and male gender (adjusted OR, 3.76; 95%CI, 1.23–11.53) were associated with higher risk for myelopathy. An mRS score ≤ 2 at presentation (adjusted OR, 0.25; 95%CI, 0.09–0.71) and an associated aneurysm (adjusted OR, 0.16; 95%CI, 0.06–0.43) were protective factors. Presentation with myelopathy (adjusted OR per score, 4.73; 95%CI, 1.31–17.12) was an independent risk factors for unfavorable neurological status in untreated CCJ-AVF.Conclusion This study identifies risk factors associated with SAH, myelopathy, and unfavorable neurological status at presentation in patients with CCJ-AVF. These findings may help guide management and treatment decisions for these complex vascular malformations.