Heterozygous loss-of-function variants in heterogeneous nuclear ribonucleoprotein U (HNRNPU) cause early-onset developmental and epileptic encephalopathy with multiple congenital anomalies. Limited clinical information is currently available on HNRNPU-related neurodevelopmental disorder. The patient was a 1-year-old Japanese girl with developmental delay, hypotonia, early-onset epilepsy, respiratory distress, and distinctive facial features, including ptosis, epicanthus, a prominent nasal bridge, a wide nasal floor, a cleft soft palate, and micrognathia. Respiratory distress was caused by pharyngeal stenosis and laryngomalacia, which gradually worsened, necessitating a scheduled tracheostomy at 1 year and 7 months of age. We performed whole-exome sequencing and identified a novel de novo nonsense variant in HNRNPU. We herein describe the first case of HNRNPU-related neurodevelopmental disorder with severe airway anomalies and a novel nonsense variant, thereby expanding the phenotypic spectrum.