We present a case of a 2-month-old patient with CHARGE syndrome, cerebral haemorrhage and bilateral congenital choanal atresia (CCA). He was admitted to our otorhinolaryngology unit to solve his congenital bilateral choanal atresia proposing a transnasal endoscopic surgery. A study of CT of the skull showed that the air column was interrupted on both sides of nasal cavities; a nasal endoscopy with neonatology flexible optics showed the presence of a membrane and bony structure obstructing the passage into the nasopharynx. Preoperative brain magnetic resonance (MRN) has been made. We decided to carry out a transnasal endoscopic neuronavigation approach with multi-flaps without stenting apposition to solve the CCA, using a 0° 2.7-millimetre rigid endoscopic and Skeeter-type drill with a 2.3-millimetre microblade cutter. Postoperative nasal care was essential to avoid recurrences. Endoscopic follow-up was performed; a large uni-neochoane was residual at 3 months, all raw surfaces were covered by multiple mucosal flaps welded with fibrin.