Advanced engine design and alternative fuels present the possibility of fuel injection at purely supercritical conditions in diesel engines and gas turbines. The complex interactions that govern this phenomenon still need significant research, particularly the boundary conditions for fuel injection are critical for accurate simulation. However, the flow inside the injector itself is often omitted to reduce the computational efforts, and thus, velocity, mass flux, or total pressure is specified at the injector exit (or domain inlet), often with simplified velocity profiles and turbulence levels. This simplified inlet boundary treatment has minimal effects on results for conventional fuel injection conditions, however, the validity of this approach at supercritical conditions has not been assessed. Comprehensive real-gas and binary fluid mixing models have been implemented for computational fluid dynamics (CFD) analysis of fuel-air mixing at supercritical conditions. The model is verified using prior CFD results from the literature. The model is used to investigate the effects of the shape of axial velocity and mass fraction profiles at the inlet boundary with the goal to improve the comparison of predictions to experimental data. Results show that the boundary conditions have a significant effect on the predictions, and none of the cases match precisely with experimental data. The study reveals that the physical location of the inlet boundary might be difficult to infer correctly from the experiments and highlights the need for high-quality, repeatable measurements at supercritical conditions to support the development of relevant high-fidelity models for fuel-air mixing.