In this paper a time-domain numerical model for describing the presence of vorticity and entropy boundary layers is introduced. The boundary model can be inserted in acoustic time-domain models such as the finite-difference time-domain (FDTD) model for studying the acoustic behavior of high-quality resonator structures. The main focus in deriving the model is on numerical efficiency. Boundary layer theory is reviewed to obtain a three-dimensional formulation of its influence on FDTD equations that must be applied in boundary discretization cells. Theωdependence that is encountered is approximated in time domain in such a way that no numerical convolution is required. Although this approximation is rather inaccurate, it is sufficient for most applications and introduces almost no extra computational effort. Several numerical examples illustrate the applicability of the model.