Focal stroke during the perinatal and neonatal period is a significant cause of cognitive and behavioral deficits. Currently, the number of models available to study neonatal brain injury is limited and many are technically difficult to induce in neonatal rodents. We demonstrate a reproducible method to induce a focal ischemic injury in the cerebral cortex of neonatal mice that utilizes the principle of photothrombosis. Postnatal day 7 pups were anesthetized and systemically administered rose bengal (50 mg/kg). Permanent focal ischemia was induced in the medial frontal cortex and somatosensory cortex by irradiating surface blood vessels with a laser (532 nm). By placing a mask having an aperture of defined shape and size on the skull surface, we were able to reliably and reproducibly induce infarcts in discretely defined cortical regions. Further, we demonstrate explicit control of infarct volume by modifying the duration of laser exposure. This tool will provide a means for researchers to safely, easily and noninvasively induce reproducible ischemic lesions in specified regions of the neonatal cortex.