The presence of antiphospholipid antibodies is associated with arterial and venous thrombosis. A 14-year-old girl, with systemic lupus erythematosus (SLE), developed headache and cough and was found to have intracranial venous sinus thrombosis with secondary pulmonary embolism associated with antiphospholipid syndrome. Clinical and radiological improvement occurred with anticoagulation therapy. Because SLE is commonly associated with antiphospholipid antibodies, thromboembolic events should be considered in the differential diagnosis of both cough and headache in children with SLE.