Background Primary ciliary dyskinesia (PCD) is generally likened to cystic fibrosis (CF) due to similarities in impaired mucociliary clearance and some other symptoms. The aim of our study was to investigate pulmonary and extrapulmonary characteristics of children with CF and PCD since no studies have addressed respiratory muscle strength in children with PCD and to compare the results to those obtained from healthy age-matched controls. Methods Pulmonary and extrapulmonary characteristics were assessed by 6-min walk test, spirometry, maximum inspiratory and expiratory pressure measurements, and knee extensor strength test in the children with CF, PCD, and healthy controls. Results Children with PCD and CF had similar PFT results, except forced expiratory flow between 25% and 75% of vital capacity (FEF25-75) which was lower in PCD (p = .04). Maximum inspiratory pressure (MIP) value was lower in the children with CF compared with the healthy controls (p = .016), MEP value of the children with PCD was worse than those with CF and healthy controls (p = .013 and p = .013), respectively. 6-min walk test (6MWT) distance of the children with CF was lower than their healthy counterparts (p = .003). Knee extensor muscle strength differed among the children with PCD, CF, and healthy control groups, but post hoc test failed to show statistical significance (p = .010). Conclusion Children with CF and PCD had some impairments in pulmonary functions, respiratory muscle strength, functional capacity, and peripheral muscle strength compared with healthy children. However, the unique characteristics of each disease should be considered during physiotherapy assessment and treatment. The clinicians may especially focus on the respiratory and peripheral muscle strength of the children with PCD.