Mesoporous silicon (MePSi) is a promising material for future microelectronic chip multifunctionalization systems and for microsensing devices. In addition to the electrical characteristics, the thermal properties of MePSi layers affect the heat dissipation and the thermal management in related microelectronic devices. In this study, the thermal properties of n-type MePSi, prepared by electrochemical etching, have been investigated using the pulsed photothermal method. SEM observations evidence a columnar structure of pores, whose size varies between 5 and 25 nm, for the different etching depths (0.2, 1, 10, and 50 μm). Also, Fourier transform infrared (FTIR) spectroscopy has highlighted the presence of Si–H and Si–O bonds in addition to the confirmation of the porosity values and their size distribution. By means of the pulsed photothermal method (PPT), the thermal properties of MePSi such as thermal conductivity (k), volume specific heat (ρCp), and thermal contact resistance (Rth) have been determined. The thermal conductivity decreases from 8.0 to 5.0 W·m–1·K–1 as increasing the etching depth from 0.2 to 50 μm. Opposite to the monocrystalline-Si samples, the presence of Si–H and Si–O bonds in the MePSi in addition to the porosity effect is responsible for the drop of the thermal conductivity values.