Congenital choanal atresia (CCA) is the developmental failure of the nasal cavity to communicate with nasopharynx. Surgical repair is recommended in the first weeks of life in bilateral cases because this is a life-threatening situation in newborns. This is a case report of a full-term, healthy newborn baby presenting with intermittent attacks of cyanosis and respiratory distress soon after birth. On examination, alternating cyanosis and normal colour was observed in the infant. The insertion of nasal catheters in both the nares revealed the diagnosis of bilateral CCA. For this rare condition, conservative management was followed with elective transnasal endoscopic repair to relieve the life threatening nasal obstruction at the tenth day of life.