Background: Joubert syndrome is a rare autosomal recessive ciliopathy characterized by distinctive hindbrain malformations. The clinical presentation in the neonatal period, including respiratory dysregulation and hypotonia, can mimic perinatal asphyxia, leading to diagnostic delay and misattribution of neurodevelopmental outcomes. Case Presentation: We report a female infant, fourth in birth order, born to a consanguineous couple, who presented with neonatal depression requiring bag-mask ventilation. At four months, absence of social smile and neck holding prompted neuroimaging, which revealed cerebellar vermian hypoplasia with the pathognomonic bat-wing configuration of the fourth ventricle, consistent with Joubert syndrome. The infant had progressive microcephaly (head circumference <−3 SD) with developmental quotient of 48 on standardized assessment. Systemic evaluation was unremarkable except for a mild atrial septal defect. The child succumbed at eighteen months of age. Conclusion: This case illustrates how Joubert syndrome can masquerade as perinatal asphyxia. The perinatal depression likely reflected intrinsic brainstem-cerebellar dysfunction rather than hypoxic-ischemic injury. Clinicians should maintain a high index of suspicion for congenital neurodevelopmental disorders when developmental trajectories deviate from expected recovery patterns, especially in consanguineous families. Keywords: Joubert syndrome; perinatal asphyxia; diagnostic pitfall; molar tooth sign; bat-wing ventricle; consanguinity; ciliopathy