A method and system for non-invasive hemodynamic assessment of coronary artery stenosis based on medical image data is disclosed. Patient-specific anatomical measurements of the coronary arteries are extracted from medical image data of a patient. Patient-specific boundary conditions of a computational model of coronary circulation representing the coronary arteries are calculated based on the patient-specific anatomical measurements of the coronary arteries. Blood flow and pressure in the coronary arteries are simulated using the computational model of coronary circulation and the patient-specific boundary conditions and coronary autoregulation is modeled during the simulation of blood flow and pressure in the coronary arteries. A wave-free period is identified in a simulated cardiac cycle, and an instantaneous wave-Free Ratio (iFR) value is calculated for a stenosis region based on simulated pressure values in the wave-free period.
