This paper reports the cross-plane thermal conductivity of ordered polycrystalline mesoporous silicon thin films between 30 and 320 K. The films were produced by a combination of evaporation induced self-assembly (EISA) of mesoporous silica followed by magnesium reduction. The periodic ordering of pores in mesoporous silicon was characterized by a combination of 1D X-ray diffraction, 2D small angle X-ray scattering, and direct SEM imaging. The average crystallite size, porosity, and film thickness were about 13–18 nm, 25–35%, and 140–260 nm, respectively. The pores were arranged in a face-centered cubic lattice. Finally, the cross-plane thermal conductivity of the meso-porous silicon thin films was measured using the 3ω method. The measured thermal conductivity was about 3 to 5 orders of magnitude smaller than that of the bulk dense crystalline silicon for the temperature range considered. The effects of temperature and film thickness on the thermal conductivity were investigated.