Isolated left ventricular non-compaction (ILVNC) is a rare congenital cardiomyopathy and is associated with arrhythmias, heart failure and thromboembolism including ischaemic stroke. Pregnancy is a relative contraindication to thrombolysis for acute ischaemic stroke, although case reports suggest the treatment can be given in selected cases. We report a case of recurrent cryptogenic strokes in a 36-year-old female who was thrombolysed with good outcome at 37 weeks' gestation and was eventually found to have ILVNC as the cause. She had a predilection to recurrent posterior circulatory strokes due to foetal posterior communicating arteries. To our knowledge this is the first case report of safe thrombolysis for acute ischaemic stroke in pregnancy caused by ILVNC.