We are presenting a case report of a previously healthy 39-year-old man who was found to have acute inferior ST-elevation myocardial infarction (STEMI) and acute large right middle cerebral artery (MCA) ischemic stroke with hemorrhagic transformation. Transesophageal echocardiogram and chest CT angiogram revealed two thrombi; one attached to the wall of the ascending aorta just above the right coronary artery sinus, and one at the origin of the brachiocephalic trunk. The occlusion of the coronary artery and right MCA most likely could be because of embolization from these thrombi. Extensive workup looking for underlying etiology and risk factors for these concurrent vascular events in this young man revealed hyperhomocysteinemia along with unfavorable lipid profile, and family history of premature coronary artery disease which increased the suspicion of familial hypercholesterolemia. Besides, the presence of vitamin B12 and folate deficiencies. The elevated serum homocysteine is likely a major risk factor for thromboembolism in this patient. The patient received antithrombotics and vitamin supplementations and gradually improved without any worsening of the stroke's hemorrhagic transformation. We suggest that hyperhomocysteinemia needs to be considered in the differential etiology of vascular events in young people or those with no significant history of major vascular risk factors. Besides, vitamin supplementation could be a cost-effective, safe, and efficient way to decrease elevated serum homocysteine levels and prevent vascular complications. As well as this case report demonstrates that antithrombotics can safely be used after stroke's hemorrhagic transformation without neurological deterioration or aggravation of hemorrhagic transformation.