Neurological injury remains a major concern during neonatal aortic arch surgery. Near-infrared spectroscopy (NIRS) is commonly used to monitor cerebral oxygenation but does not provide direct quantitative information on cerebral blood flow. Transit-time flow measurement (TTFM) allows real-time volumetric flow assessment and may represent an additional tool for intraoperative monitoring of cerebral perfusion. We report the intraoperative use of TTFM for continuous monitoring of cerebral inflow during the repair of an interrupted aortic arch in a neonate. A perivascular flow probe was placed around the left common carotid artery to allow real-time measurement of carotid flow during cardiopulmonary bypass and selective cerebro-myocardial perfusion. Baseline flow in the brachiocephalic trunk was approximately 87 ml/min. During selective cerebro-myocardial perfusion, carotid flow remained stable at 45–50 ml/min. After aortic clamping, the carotid waveform changed from pulsatile to continuous, with a reduction in pulsatility index from 1.5 to 0.6. Flow values remained stable throughout arch reconstruction and were consistent with arterial pressure and NIRS monitoring. Transit-time flow measurement enabled direct real-time assessment of cerebral inflow during neonatal arch repair and provided quantitative information complementary to conventional monitoring. This technique may represent a useful adjunct for evaluating cerebral perfusion during complex neonatal cardiac surgery.