Acute internal jugular vein thrombosis (IJVT) is a rare vascular disease that can cause lethal complications and manifests with varying neurological symptoms. A 42‑year‑old woman presented with a progressively worsening headache over the left temporal‑occipital area and pain in the left posterior nuchal; ultrasonography and magnetic resonance venography (MRV) revealed a thrombosis with critical stenosis in the left internal jugular vein (IJV). Seven days after treatment with an anticoagulant, she exhibited considerable improvement. Follow‑up ultrasonography and three‑dimensional computed tomography angiography (CTA) indicated spontaneous IJV recanalization. To avoid implementing inappropriate treatments and prevent adverse outcomes, acute IJVT should be considered as a cause of secondary headaches. To determine the prognosis and secondary prophylaxis strategy (i.e., medical or surgical), recanalization should be detected using color‑coded duplex ultrasonography and confirmed using MRV or CTA; these are all safe and minimally invasive procedures.