Studies have shown that respiratory muscle training enhances functional capacity and pulmonary function in Fontan patients. However, diaphragm muscle characteristics in Fontan children have not been fully elucidated. The aim of this study was to compare respiratory function, maximal and submaximal functional capacities, and quality of life, as well as to assess diaphragm mobility and thickness, between Fontan patients aged 8 to 12years and healthy individuals. This cross-sectional study included 45 children-27 Fontan patients, Fontan Group (FG) and 18 healthy control Group (CG) subjects. Different examinations were performed: spirometry was used to analyze pulmonary volume and capacity; manovacuometry was used to determine respiratory muscle strength; chest ultrasound was used to determine diaphragm muscle characteristics; cardiopulmonary exercise and the six-minute walk test (6MWT) wereused to determine functional capacity; the AUQEI questionnaire was used to determine quality of life. Descriptive analysis and intergroup comparisons were performed for all the data. Compared with the CG, the FG exhibited impaired pulmonary function and reduced functional capacity. Significant differences in median values were noted for forced expiratory volume in one second (FEV1): 2.39L/min, p = 0.002; forced vital capacity (FVC): 1.73 vs. 3.06L/min, p = 0.002; maximal inspiratory pressure: - 73 vs. - 117cmH2O, p = 0.007; absolute peak VO2: 1.09 vs. 1.51L/min, p < 0.001; relative peak VO2: 31.9 vs. 42.5mL/kg/min, p = 0.003; and 6MWT distance: 420 vs. 586m, p < 0.001. Diaphragmatic thickness, mobility and quality of life were similar between the groups. Despite the reduced functional capacity, impaired pulmonary volume and capacity, and respiratory muscle weakness of the FG compared to those of the CG, the diaphragm characteristics and quality of life were similar between the groups.