The bidirectional cavopulmonary anastomosis (BCPA or bidirectional Glenn) is an operation to treat congenital heart diseases of the right heart by diverting the systemic venous return from the superior vena cava to both lungs. The main goal is to provide the correct perfusion to both lungs avoiding an excessive increase in systemic venous pressure. One of the factors which can affect the clinical outcome of the surgically reconstructed circulation is the amount of pulsatile blood flow coming from the main pulmonary artery. The purpose of this work is to analyse the influence of this factor on the BCPA hemodynamics. A 3-D finite element model of the BCPA has been developed to reproduce the flow of the surgically reconstructed district. Geometry and hemodynamic data have been taken from angiocardiogram and catheterization reports, respectively. On the basis of the developed 3-D model, four simulations have been performed with increasing pulsatile blood flow rate from the main pulmonary artery. The results show that hemodynamics in the pulmonary arteries are greatly influenced by the amount of flow through the native main pulmonary artery and that the flow from the superior vena cava allows to have a similar distribution of the blood to both lungs, with a little predilection for the left side, in agreement with clinical postoperative data.