Brainstem disconnection is a very rare neonatal abnormality, with only seven cases reported. We report a unique case of a neonate who presented at delivery with hypertonia, dysmorphic facial features, and respiratory distress, as well as numerous musculoskeletal and genitourinary abnormalities. MRI of the brain showed disconnection between the pons and medulla with cerebellar hypoplasia and absent cerebellar peduncles. It aided in the description of the neurological and vascular anomalies associated with this diagnosis.