Homocystinuria is a treatable autosomal recessive inherited disorder. This condition may cause life-threatening complications such as thromboembolic events. Coronavirus disease 2019 (COVID-19) is associated with an increased risk of venous thromboembolic events. Here, we report a case of late diagnosis of homocystinuria presenting with deep venous thrombosis and COVID-19. This study highlights a sustained high index of suspicion for homocystinuria to prevent severe thromboembolic complications.