Eosinophilic cystitis (EC) is rather an uncommon disease in childhood. A case of EC in a 5-year-old boy, in which open biopsy was needed for final diagnosis, is reported. After diagnosis, he was treated with pemirolast potassium followed-up with eosinophil cationic protein (ECP) in serum and urine. Eosinophil cationic protein is an appropriate marker of EC.