This paper is concerned with computational modeling of a severe congenital defect called Hypoplastic left heart syndrome (HLHS) that is the most common cardiac malformation with the highest likelihood of deaths in newborns. A lumped parameter model of the HLHS circulation has been developed to study the hemodynamic variables in the various sections of the cardio-pulmonary circulation system. We applied a short-term, cycle-averaging operation to the differential equations of the HLHS model to obtain the cycle-averaged model. Study has been carried out to analyze the variation of blood flow rate in different parts due to parameter changes. Results show that the developed model, could bring a good insight into understanding of the HLHS disease.