Industry-standard lyophilization practices for protein-based therapeutics face a critical bottleneck, where product cycle development relies on empirical testing to check for the thermal and mechanical limits. This project develops a COMSOL-based multiphysics model to describe the coupled heat and mass transfer processes occurring during the primary drying phase of lyophilization. Freeze-drying involves ice sublimation during primary drying and the removal of residual ice-bound water during secondary drying, both of which depend on temperature history under vacuum. However, the bulk of the process occurs during the primary drying phase, which is why that is the focus of our model. Because extreme temperatures can damage protein structure and insufficiently low temperatures slows drying, the process presents a trade-off between product stability and manufacturing efficiency. The model solves three coupled transient equations for ice concentration, temperature, and vapor density in a cylindrical porous vial considering shelf heat conduction, vapor transport, and sublimation. The model computed a drying time of 24.3 hours and revealed that shelf temperature had the most dominant effect on drying time. Validation with published experimental data within 5% supports the model’s utility for informing lyophilization process design without wasting product or time.