Introduction Assessment of exercise capacity is important for information about lung function and prognosis in primary ciliary dyskinesia (PCD). In addition, deterioration in the pulmonary system may affect cough efficiency, posture, and thoracoabdominal mobility. In turn, this deterioration may also disturb the psychological function of patients with PCD. Therefore, this study aimed to compare exercise capacity, cough strength, thoracoabdominal mobility, posture, and depression in children with PCD and healthy peers. Methods Twenty-seven patients with PCD and 28 healthy peers were included. Aerobic exercise capacity (3-min step test), cough strength (peak expiratory flow meter), thoracoabdominal mobility (upper chest, lower chest, and abdomen), posture (Corbin postural assessment scale), and depression (Children's Depression Inventory) were evaluated. Results Patients' number of steps completed, cough strength, and thoracoabdominal mobility were significantly decreased; total posture and depression scores were higher compared with healthy controls (p< 0.05). There was a significant relationship between cough strength and maximal expiratory strength (r = 0.541, p= 0.004) and total number of steps (r = 0.509, p= 0.007) in the patients. Conclusion Aerobic exercise capacity, cough strength, and thoracoabdominal mobility were impaired, posture was deteriorated, and depression perception elevated in children with PCD compared to healthy peers. Furthermore, aerobic exercise capacity and maximal expiratory strength are related to cough strength in these patients. Rehabilitation programs including aerobic and resistive exercise training, deep breathing and postural exercise, and nutrition counseling may improve these results and better be investigated. Trial registration: : NCT03370029; December 12, 2017.