Choanal atresia is an uncommon malformation of the upper airway. Bilateral choanal atresia usually detected earlier as it is often associated with severe asphyxia immediately after birth. The diagnosis is often delayed in unilateral type, and mostly presented with unilateral chronic nasal discharge. This condition is rarely encountered but should be considered as a possible differential diagnosis of persistent nasal discharge. We present a case of unilateral congenital choanal atresia in a 4-month-old baby girl presented with persistent unilateral nasal discharge. Diagnostic investigation and possible surgical treatment techniques were discussed.