Most previous models of vapour absorption in the respiratory tract have assumed steady state flow fields and steady state diffusion into the airway walls. However, recent studies have shown that transient absorption flux into the walls of the upper airways can significantly influence predicted uptake or deposition values. The disadvantage of accounting for transient absorption into the airway walls is a more complex boundary condition and numerical model. The objective of this study was to evaluate the effects of both transient flow fields and transient mass absorption on the uptake of highly and moderately soluble compounds in an upper airway model. The geometry consisted of the mouth-throat region coupled with a multilayer wall model containing air, mucus, tissue, and blood phases. Based on previous studies, a boundary condition that represents transient absorption into the airway walls was applied. A new dosimetry program, named transient absorption of chemical species (TAOCS) 1.0, was developed and implemented to determine the coefficients needed for the transient boundary condition expression and to apply the boundary condition to the computational fluid dynamics (CFD) model. Both steady state and transient conditions were considered for the airflow field and wall absorption. The case of perfect wall absorption with a zero surface concentration was also considered. Results indicated that steady state airflow provided a reasonable approximation to transient airflow conditions in terms of total and local deposition (values within 10-30%). However, the simulation of transient wall absorption was critical unless the compound was highly soluble (with a mucus-air partition coefficient ≥320), in which case a perfect absorption boundary condition was accurate to within a relative difference of 50%. Still, the perfect absorption boundary condition did not accurately capture local deposition enhancement factor values. Based on these findings, implementation of the transient absorption boundary condition appears critical to predict local deposition characteristics for even highly soluble compounds. Use of the TAOCS program simplified the implementation of the complex transient absorption condition making the CFD simulation process more efficient and user-friendly.