Contactin-associated protein (CNTNAP1) gene mutations have been reported in cases of congenital hypomyelinating neuropathy (CHN), a rare hereditary neuropathy. We present a case of a term male infant born at 39 weeks 4 days with respiratory distress, impaired swallow function, and hypotonia. Neurological workup for structural, autoimmune, neuromuscular, and metabolic etiologies was negative and whole exome sequencing revealed a novel mutation in the CNTNAP1 gene, consistent with a diagnosis of CHN3. While CHN3 cases with mutations in the same domain have required long-term respiratory support, our patient, now 2 years old, has not required respiratory support since his initial birth hospitalization. Neurologically, he now has central hypotonia with hypertonia in the bilateral extremities and global developmental delay. This case adds to a growing number of identified pathological CNTNAP1 mutations and their heterogenous clinical phenotypes and highlights a rare neurological etiology for respiratory distress in newborns.