A 7-month-old female spayed domestic shorthair cat was presented for investigation of stertor, open mouth breathing without apparent distress, and chronic bilateral nasal discharge that was unresponsive to antibiotics. Complete bilateral bony choanal atresia was diagnosed with computed tomography and nasopharyngoscopy. Choanal atresia is an uncommon congenital condition where the choana (nasal passage into the nasopharynx) is blocked by abnormal bone or soft tissue uni- or bilaterally. The cat's clinical signs improved dramatically immediately after trans-palatal surgical correction. Post-surgical complications included the development of nasopharyngeal scar tissue and subsequent stenosis, persistent right-sided nasal discharge, and permanent damage to the right eye (blindness and cataract formation). Nasopharyngeal stenosis was managed with repeated balloon dilatations and temporary stenting, and the owner reported an excellent quality of life at 8-month follow-up. Bilateral bony choanal atresia has not been previously reported in cats. Uni- or bilateral choanal atresia should be considered in young cats presenting with refractory stertor, chronic nasal discharge, and/or open mouth breathing.