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Acute brain injury (ABI) is a frequent complication of pediatric extracorporeal membrane oxygenation (ECMO) that could be detected by continuous neuromonitoring. Cerebral near-infrared spectroscopy (NIRS) allows monitoring of cerebral oxygenation. To assess whether an impaired cerebral oxygenation was associated with short-term outcome during pediatric ECMO. We conducted a single-center retrospective study in a pediatric intensive care unit. Children under 18 years old were included if receiving veno-venous or veno-arterial ECMO with concurrent NIRS monitoring. Cerebral saturation impairment was defined as rScO2 under 50% or 20% from the baseline for desaturation, and above 80%. Cerebral imaging (magnetic resonance imaging or CT scan) was performed in case of neurological concern. A radiologist blinded for patient history identified ABI as any hemorragic or ischemic lesion, then classified as major or minor. Primary endpoint was the outcome at hospital discharge. Poor outcome was defined as death or survival with a pediatric cerebral performance category scale (PCPC) score ≥ 3 and/or a major ABI. Good outcome was defined as survival with a PCPC score ≤ 2 and/or a minor or no ABI. Secondary endpoint was mortality before PICU discharge. Sixty-three patients met inclusion criteria; 48 (76%) had veno-arterial ECMO. Mortality rate was 51%. Forty-eight of sixty-three patients (76%) evolved with a poor outcome, including 20 major ABI. Mean rScO2 in the right/left hemisphere was 73 ± 9%/75 ± 9%. Cerebral desaturation and decline of rScO2 below 20% from the baseline, regardless of side, were each associated with poor outcome (multivariable-adjusted odds ratio (OR), 4 [95%CI 1.2; 15.1], p = 0.03, and 3.9 [95%CI 1.1; 14.9], p = 0.04, respectively), as well as a mean right rScO2 80% seemed to be protective. NIRS monitoring might be included within multimodal neuromonitoring to assess the risk of the brain injury related to pediatric ECMO.