Introduction This case report illustrates the complexities of arrhythmogenic right ventricular cardiomyopathy (ARVC) and its thromboembolic complications resulting in top-of-basilar artery syndrome. We discuss the case of a 37-year-old male with ARVC who presented with acute onset of dizziness, imbalance, and vomiting, leading to the diagnosis of a top-of-basilar artery occlusion which was successfully treated. Case presentation This case highlights the diagnostic and acute treatment challenges in basilar artery occlusion (BAO) due to its non-specific symptoms and emphasizes the critical role of CT angiography in detecting occlusive thrombi for timely intervention. With prompt endovascular thrombectomy and bridging intravenous thrombolysis, complete recanalization was achieved and the patient was discharged with modified Rankin Scale (mRS) of 1. Effective management strategies involve assessing ventricular function, detecting arrhythmias, identifying intracardiac thrombi, and implementing individualized stroke prevention measures, such as using direct oral anticoagulants(DOACs). Conclusion: This study illustrates the necessity of a multidisciplinary approach in optimizing patient outcomes in acute stroke care. Focusing on the rare condition of ARVC and the specific challenge of top-of-basilar artery occlusions in this case underscores the intricate interplay between cardiovascular and cerebrovascular pathology leading to improved understanding and management of these conditions.