Vascular complications particularly splanchnic vein thrombosis can occur in acute as well as chronic pancreatitis, but extra-splanchnic thrombosis occurs rarely. We report a rare case of acute pancreatitis complicated by isolated internal jugular vein thrombosis. A 26-year-old Indian woman presented with complaints of severe epigastric pain radiating to the back, vomiting, and abdominal distension. Investigations showed low hemoglobin and serum calcium, and a raised serum amylase and lipase. Contrast-enhanced computerized tomography (CECT) of the abdomen suggested acute pancreatitis with bilateral pleural effusion and mild ascites. The patient was managed for acute pancreatitis with antibiotics, analgesics, pantoprazole, and other supportive treatment. She subsequently developed pain and swelling on the right side of the neck. Ultrasound Doppler examination of the neck revealed an isolated thrombus in the right internal jugular vein (IJV). The patient was started on enoxaparin and transitioned to warfarin. The patient improved symptomatically and was discharged on warfarin. A follow-up ultrasound Doppler examination showed a partial resolution of the clot. The patient was maintained on oral anticoagulants for 6 months. Isolated IJV thrombosis may complicate acute pancreatitis. A timely diagnosis and prompt treatment are critical for a positive outcome.