Recently, we have presented and experimentally validated a unique numerical solver of the coupled radiative transfer equations (RTEs) for rapidly computing time-dependent excitation and fluorescent light propagation in small animal tomography. Herein, we present a time-dependent Monte Carlo algorithm to validate the forward RTE solver and investigate the impact of physical parameters upon transport-limited measurements in order to best direct the development of the RTE solver for optical tomography. Experimentally, the Monte Carlo simulations for both transport-limited and diffusion-limited propagations are validated using frequency domain photon migration measurements for 1.0%, 0.5%, and 0.2% intralipid solutions containing 1 microM indocyanine green in a 49 cm3 cylindrical phantom corresponding to the small volume employed in small animal tomography. The comparisons between Monte Carlo simulations and the numerical solutions result in mean percent error in amplitude and the phase shift less than 5.0% and 0.7 degrees, respectively, at excitation and emission wavelengths for varying anisotropic factors, lifetimes, and modulation frequencies. Monte Carlo simulations indicate that the accuracy of the forward model is enhanced using (i) suitable source models of photon delivery, (ii) accurate anisotropic factors, and (iii) accurate acceptance angles of collected photons. Monte Carlo simulations also show that the accuracy of the diffusion approximation in the small phantom depends upon (i) the ratio d(phantom)/l(tr), where d(phantom) is the phantom diameter and l(tr) is the transport mean free path; and (ii) the anisotropic factor of the medium. The Monte Carlo simulations validates and guides the future development of an appropriate RTE solver for deployment in small animal optical tomography.