A free-floating carotid artery thrombus is a very rare ultrasonographical finding in patients with acute ischemic cerebrovascular events. One of the main causes of this presentation is represented by the hypercoagulability status of the patients. We report the case of a young male patient who presented with several transient ischaemic attacks secondary to a mobile thrombus in the left carotid sinus. Two hematological abnormalities, essential thrombocytosis and methylene tetrahydrofolate reductase mutation were found to be related to the thrombus formation. The role of the latter in the pathogenesis of ischemic stroke is not well documented in the literature. Following antiplatelet and anticoagulant medication, there was a fast dissolution of the thrombus, followed by a favorable clinical outcome. Neurologists should be aware that young patients with stroke require extensive imagistic and laboratory screening for an accurate etiological diagnosis.