Internal jugular vein (IJV) thrombosis is mainly related to central venous catheter, malignancy, and ovarian hyperstimulation syndrome. We report a case of IJV thrombosis possibly related to IJV compression between the styloid process and the first cervical vertebra (C1) transverse process. To support this hypothesis, we perform radiological assessment of the IJV and examine its relationship with the styloid process and C1 transverse process in 34 controls. Our results showed a strong correlation between IJV diameter and styloid process–C1 transverse process distance. Compared to control subjects, our patient had a short styloid process–C1 transverse process distance, which suggests its involvement in IJV thrombosis.