A 25-year-old, 7-weeks pregnant woman was admitted to the Nagaoka Red Cross Hospital in a state of confusion, following fever, headache and vomiting. Brain CT and MRI showed swelling in the bilateral thalami, basal ganglia and splenium of corpus callosum, and thrombosis of the internal cerebral veins and straight sinus. Initial treatment by intravenous heparin and glycerol was successful, and she regained her consciousness, leaving antegrade amnesia and childish character change. Her free protein S antigen was 32% (normal 60-127) and subsequently rose to 70% after delivery. She was diagnosed as having secondary protein S deficiency associated with pregnancy. Because warfarin can be teratogenic, subcutaneous heparin injection was prescribed in order to prevent thrombosis and the patient subsequently had a successful delivery. This was the first case in Japanese of successful delivery after subcutaneous heparin treatment in a patient with cerebral venous thrombosis.