Ischemic stroke associated with rare clinical syndromes represents less than 5% of etiologic factors. From those syndromes are Holt-Oram syndrome and Left ventricular non-compaction syndrome. We report a case of a 66 years old male with genetically confirmed Holt-Oram syndrome due to TBX5 mutation who presented with cryptogenic stroke most likely due to cardioembolic etiology. The patient has a history of moderate nonischemic cardiomyopathy due to an atypical pattern of left ventricular non-compaction confirmed by Cardiac Magnetic Resonance Imaging. The patient was treated appropriately with thrombolytic therapy and catheter-directed mechanical thrombectomy with minimal residual stroke symptoms. Holt-Oram syndrome is a genetic condition with variable clinical phenotypes, including cardiac manifestations. Left ventricular non-compaction syndrome is rare congenital cardiomyopathy defined as prominent left ventricular trabeculae, deep intertrabecular recesses, and a thin compacted layer. And only a few cases were reported with both conditions. Therefore, patients with the Holt-Oram Syndrome should get a comprehensive cardiac evaluation to exclude non-compaction cardiomyopathy, which may have significant prognostic implications.