Abdominal aortic aneurysm (AAA) is a pathological condition characterised by localised dilation of the infrarenal aorta, which can be fatal if rupture occurs. Current diagnostic criteria for repair are not patient-specific, but computational modelling may help to predict the potential growth and risk of AAA rupture accurately. This paper highlights how important using the Windkessel effect and fully-developed inflow velocity framework for the biomechanical analysis of AAA is; in other words, this research investigates how different boundary conditions in modelling methods affect the ability to correctly represent the biomechanics of AAA with complex non-linear parameters using a two-way fluid–structure interaction (FSI) technique. Time-averaged wall shear stress (TAWSS) is highly sensitive to boundary conditions, so unrealistic or simplified boundary conditions can lead to very different TAWSS results. This study also revealed that the use of outflow 3-element Windkessel boundary conditions on pulsatile pressure affects the flow pattern and increases the flow recirculation period. By accounting for the Windkessel effect and preventing backflow in numerical studies of AAA, the maximum displacement found in the distal branches can also be reduced. Models assuming plug velocity profiles overestimate peak wall stress by approximately 20% compared with models using fully developed parabolic inlet velocity profiles. This study incorporated a three-layer anisotropic material model and non-Newtonian fluid properties into the simulation, providing a more realistic representation of the effect of boundary condition selection on AAA mechanics. The results summarised from the parametric study could contribute to better prediction of AAA growth and rupture risk, and have important implications for the development of improved treatment strategies for AAA patients.