We aimed to develop a method of CT-to-MR image synthesis to assist in detecting hypoattenuating brain lesions in acute ischemic stroke. Emergency head CT images of 193 patients with suspected stroke and follow-up MR images were collected. A generative-adversarial-network model was developed for CT-to-MR image synthesis. With synthetic MRI compared to CT, sensitivity was improved by 116% in patient detection and 300% in lesion detection, and extra 75% of patients and 15% of lesions missed on CT were detected on synthetic MRI. Our method could be a rapid tool to improve readers’ detection of hypoattenuating lesions in AIS.