To analyze the role of sensitive cardiac troponin I (scTnI) and high-sensitive troponin T (hscTnT) in the determination of myocardial injury caused by volume and pressure load due to pulmonary hypertension (PH) and to investigate if these markers may be useful in the management of PH in childhood. Twenty-eight patients with congenital heart disease (CHD) with left to right shunt and PH, 29 patients with CHD with left to right shunt but without PH, and 18 healthy children, in total 75 individuals, were included in the study. All cases were aged between 4 and 36 months. Echocardiographic evaluation was performed in all cases, and invasive hemodynamic investigation was performed in 33 cases. Blood samples were obtained from all cases, for the measurement of brain natriuretic peptide (BNP), pro-brain natriuretic peptide (pro-BNP), sensitive cardiac troponin I (scTnI), and high-sensitive troponin T (hscTnT) levels. The mean BNP, pro-BNP, scTnI, and hsTnT levels were statistically significantly higher in patients with PH than in the patients without PH (p < 0.001). A statistically significant positive correlation was determined between pulmonary artery systolic pressure and scTnI and hscTnT levels (r = 0.34 p = 0.01, r = 0.46 p < 0.001, respectively) levels. Pulmonary hypertension determined in congenital heart diseases triggers myocardial damage independently of increased volume or pressure load and resistance, occurring by disrupting the perfusion via increasing ventricular wall tension and the myocardial oxygen requirement. Serum scTnI and hscTnT levels may be helpful markers to determine the damage associated with PH in childhood.