Full-body patient simulators provide a technological basis for clinical education without risk to real patients. In a previous study, we described a model for educational simulation of infant cardiovascular physiology. Using essentially the same methodology, we derive a mathematical model for the cardiovascular system of a healthy 1-week-old neonate. Computer simulations of this model result in vital signs that are close to target hemodynamic variables. Simulated systemic arterial pressure waveform and left ventricular pressure-volume loop are realistic, and the system reacts appropriately to blood loss. We also adapt the model structure and change its parameters to reflect the congenital heart defects: patent ductus arteriosus, tetralogy of Fallot, complex coarctation of the aorta with patent foramen ovale, and transposition of the great arteries. Simulated vital signs are again close to target hemodynamic variables. The resulting model for neonatal cardiovascular pathophysiology is an essential step in attaining a full-body, model-driven neonatal acute care simulator.