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Abstract Finite element analysis (FEA) is commonly used in orthopaedic research to estimate localised tissue stresses and strains. A variety of boundary conditions have been proposed for isolated femur analysis, but it remains unclear how these assumed constraints influence FEA predictions of bone biomechanics. This study compared the femoral head deflection (FHD), stresses, and strains elicited under four commonly used boundary conditions (fixed knee, mid-shaft constraint, springs, and isostatic methods) and benchmarked these mechanics against the gold standard inertia relief method for normal and pathological femurs (extreme anteversion and retroversion, coxa vara, and coxa valga). Simulations were performed for the stance phase of walking with the applied femoral loading determined from patient-specific neuromusculoskeletal models. Due to unrealistic biomechanics observed for the commonly used boundary conditions, we propose a novel biomechanical constraint method to generate physiological femur biomechanics. The biomechanical method yielded FHD (