In this report, a ten-year-old boy was presented with a history of chronic diarrhea, recurrent wheezing, recurrent respiratory infections, finger clubbing, and growth retardation. Due to bronchiectasis in the chest tomography, low gaita elastase levels, and symptoms and signs of the case, the patient was diagnosed with cystic fibrosis at first. Nevertheless, since the patient’s response to enzyme replacement therapy was poor, sweat test results detected at intermediate levels, and gene analysis of cystic fibrosis-associated mutations were not found. A further evaluation was performed for a differential diagnosis, and Celiac disease was the final diagnosis of the patient. Our paper highlighted that patients with cystic fibrosis symptoms should be evaluated further for Celiac disease, especially in cases resistant to standard cystic fibrosis treatment. Thus, Celiac disease must be kept in mind in differential diagnoses of cystic fibrosis patients resistant to therapy or in conditions in which cystic fibrosis diagnosis is not certain.