Various intersystem shunts are widely used methods of treatment of newborns with congenital heart disease and reduced pulmonary blood flow. Shunt placement is associated with a high risk of postoperative complications and mortality. It is possible to predict the development of some complications using mathematical modeling methods and adjust the treatment. In this study we investigated the system ''aorta – shunt – pulmonary artery''. Three kinds of shunt placement with three different diameters for three patients have been analyzed. To solve hemodynamic problems, 27 cases were investigated using the common hemodynamic indices (wall shear stress, time-averaged, oscillatory shear index, relative residence time, etc.). The dependence of pulmonary artery blood flow distribution on shunt location is shown; the preferred location differs for different patient geometries. The energy loss of 4 mm diameter shunts is almost 2 times larger that of 3 mm shunts. A patient-specific approach to the treatment of each child based on objective data can significantly reduce the number of pediatric deaths and increase the effectiveness of the rehabilitation process.