There is fusion between two leaflets in functionally bicuspid (bileaflet) aortic valves with trisinuate aortic root. The degree of fusion inversely correlates with variation in the interleaflet triangle height (“commissural height”). We aimed to determine the hemodynamics and biomechanical response in the thoracic aorta due to variations in the commissural height between fused leaflets in a bicuspid aortic valve with raphe. A three-dimensional (3D) aortic valve model was reconstructed using cardiac magnetic resonance (CMR) imaging from a patient with a normal trileaflet aortic valve. Fluid–structure interaction (FSI) simulations were used to investigate the effect of variation in commissural height between the coronary leaflets with leaflet fusion, and this was contrasted to a case with a normal trileaflet valve. Phase-contrast CMR was used for validation of the simulated hemodynamics. The aorta and leaflet tissues were treated as hyperelastic materials. In the normal trileaflet aortic valve, two counter-rotating vortex cores develop within the root at peak systole and interact with the walls of the ascending aorta. However, in the bicuspid aortic valve with fusion between the coronary leaflets, the vortex system becomes more asymmetric. This correlates with more recirculation of flow toward the fusion side of the aortic root. The peak velocity, pressure gradient, wall shear stress, and strain levels increase approximately linear with decreasing commissural height and increasing leaflet fusion. Decreasing interleaflet triangle height between the fused leaflets in bicuspid aortic valves with raphe results in linear elevation of wall shear stress at the sinutubular junction and proximal ascending aorta.