Myocardial blood flow (MBF) quantification using contrast-enhanced first-pass magnetic resonance imaging relies on the precise knowledge of the arterial input function (AIF). Due to vascular transport processes, however, the shape of the AIF may change from the left ventricle where the AIF is measured to the myocardium. We employed computational fluid dynamics simulations in a realistic model of the left circumflex artery to investigate the degree to which this effect corrupts MBF quantification. Different outlet boundary conditions were applied to examine their influence on the solution. Our results indicate that vascular transport processes in realistic coronary artery geometries give rise to non-negligible systematic errors in the MBF values. The magnitude of these errors differs considerably between the outlets of the 3D model. Moreover, outlet boundary conditions are shown to have a significant influence on the outflows at the outlets of the 3D model. In particular, the employed boundary conditions respond differently to an artificially inserted stenosis and to hyperemia condition. Finally, outlet boundary conditions are shown to have an influence on the resulting MBF value. Since MBF errors are different under rest and under hyperemia conditions, overestimation of myocardial perfusion reserve values may occur as well.