Methylenetetrahydrofolate reductase (MTHFR) gene mutations, particularly homozygous mutations, have been associated with a higher incidence of venous thrombosis, coronary heart disease, and obstetric complications. We report the case of a 41-year-old man who presented with multiple vascular thrombotic events over a period of 4–5 years, including deep vein thrombosis with pulmonary thromboembolism, cerebral venous thrombosis and posterior circulation stroke. The patient was found to have elevated serum homocysteine levels and subsequently underwent genetic testing for MTHFR mutations after other potential prothrombotic conditions were excluded. This case is notable because compound heterozygous mutations of the MTHFR gene (C677T and A1298C) were identified in association with recurrent vascular thrombotic events. Management focused on long-term anticoagulation and supplementation with vitamin B6, vitamin B12, and folic acid.