The present work aims at comparing simulations of photon transport phenomena in biological multi-layered tissues by means of two methods: a finite element code and a Monte Carlo procedure. We apply these codes to model time-dependent light propagation in multi-layered media. The physical situation refers to the case of a narrow incident laser pulse of 1 ps duration acting upon the surface of the media. Time-resolved spectra are reported for different geometries and optical properties for high media. Here, codes are applied to simulate data acquired from measurements on tissues in extremities. The results of the study provide information to calibrate the finite element characteristics for future experiences including fluorescence events in multi-layered complex systems.