Abstract Background Vitamin D deficiency occurs frequently in cystic fibrosis (CF) and non-CF bronchiectasis patients. Yet, few studies have assessed the impact of vitamin D status on the clinical outcomes in pediatric bronchiectasis. This study is designed to assess vitamin D level and determine its effect on exacerbations, bacterial colonization, and lung function in pediatric patients with CF and non-CF bronchiectasis. Results This cross-sectional case-control study assessing vitamin D level was performed in a total of sixty cases under the age of 18 years—forty cases with CF and non-CF bronchiectasis and twenty age- and sex-matched healthy controls. Associations between serum vitamin D and clinical and laboratory parameters were assessed in the patient groups. Vitamin D deficiency was more prevalent among CF and non-CF bronchiectasis patients (75%, 45%) compared to controls (10%) ( P < 0.001). In addition, vitamin D deficiency was associated with more frequent and severe pulmonary exacerbations (66.7%, 46.7%) ( P =0.033, < 0.001), chronic Pseudomonas infection (80%) ( P =0.060) among CF patients, and with lower FEV1 (66%) ( P = 0.071) among non-CF bronchiectasis. Moreover, a cutoff value of vitamin D level equal or less than 22.5 ng/ml was accurate in differentiating moderate from mild pulmonary exacerbations in both patients’ groups (AUC=0.809) ( p =0.004). Conclusions Vitamin D deficiency is not uncommon in both CF and non-CF bronchiectasis. In this population, vitamin D deficiency is associated with more frequent pulmonary exacerbations, chronic Pseudomonas infection, and worse lung function.