In subjects with functionally bicuspid aortic valves (BAVs) with fusion between the coronary leaflets, there is a natural variation of the commissural angle. What is not fully understood is how this variation influences the hemodynamics and tissue biomechanics. These variables may influence valvar durability and function, both in the native valve and following repair, and influence ongoing aortic dilation. A 3D aortic valvar model was reconstructed from a patient with a normal trileaflet aortic valve using cardiac magnetic resonance (CMR) imaging. Fluid-structure interaction (FSI) simulations were used to compare the effects of the varying commissural angles between the non-coronary with its adjacent coronary leaflet. The results showed that the BAV with very asymmetric commissures (120∘ degree commissural angle) reduces the aortic opening area during peak systole and with a jet that impacts on the right posterior wall proximally of the ascending aorta, giving rise to elevated wall shear stress. This manifests in a shear layer with a retrograde flow and strong swirling towards the fused leaflet side. In contrast, a more symmetrical commissural angle (180∘ degree commissural angle) reduces the jet impact on the posterior wall and leads to a linear decrease in stress and strain levels in the non-fused non-coronary leaflet. These findings highlight the importance of considering the commissural angle in the progression of aortic valvar stenosis, the regional distribution of stresses and strain levels experienced by the leaflets which may predispose to valvar deterioration, and progression in thoracic aortic dilation in patients with functionally bicuspid aortic valves. Understanding the hemodynamics and biomechanics of the functionally bicuspid aortic valve and its variation in structure may provide insight into predicting the risk of aortic valve dysfunction and thoracic aortic dilation, which could inform clinical decision making and potentially lead to improved aortic valvar surgical outcomes.