We sought to investigate whether echocardiography with tissue Doppler imaging identifies myocardial dysfunction in children with benign joint hypermobility syndrome (BJHS). This cross-sectional study enrolled 75 children with BJHS and 70 healthy children. We performed detailed echocardiography in individuals with BJHS without inherited connective tissue disorders. Any congenital or acquired cardiac disease was excluded by clinical and echocardiographic examination. Both groups were similar in terms of age, sex, and body mass index. The diameter of the aortic annulus and sinus valsalva were wider in patients with BJHS. There was no significant differences in ejection fraction or mitral and tricuspid annular plane systolic excursion between the two groups. Pulsed-wave Doppler-derived E/A ratios in mitral and tricuspid valves were similar in both groups. Deceleration time of early mitral inflow was prolonged in patients with BJHS. Mitral and tricuspid annulus Ea velocity were significantly lower in children with BJHS. Ea, Aa, and Ea/Aa ratios in the interventricular septum, left ventricle posterior wall, and right ventricle free wall were lower in patients with BJHS than in the control group. The E/Ea ratio was greater in patients with BJHS than in the control group. Isovolumic relaxation time and right-ventricular (RV) and left-ventricular (LV) myocardial performance indices (MPIs) were greater in patients with BJHS. This study showed the diastolic dysfunction in patients with BJHS. In addition, we detected increased LV and RV MPI. We believe that BJHS may affect proteins of the myocardial cytoskeleton and extracellular matrix.