This study reports non-equilibrium molecular dynamics (MD) simulations predicting the thermal conductivity of amorphous mesoporous silica. The heat flux was imposed using the Muller-Plathe method and interatomic interactions were modeled using the van Beest, Kramer and van Santen (BKS) potential. First, simulations were validated against results reported in the literature for dense quartz and amorphous silica. The BKS potential was found to significantly overestimate the thermal conductivity of dense amorphous silica and results depended on the length of the simulation cell. Then, highly ordered pores were introduced in an amorphous silica matrix by removing atoms within selected areas of the simulation cell. Effects of the simulation cell length, pore size, and porosity on the thermal conductivity were investigated at room temperature. Results were compared with predictions from commonly used effective medium approximations as well as with previously reported experimental data for films with porosity and pore diameter ranging from 20% to 48% and 30 to 180 Å, respectively. Predictions of MD simulations overestimated the experimental data and agreed with predictions from the coherent potential model. However, MD simulations confirmed that thermal conductivity in sol-gel amorphous mesoporous materials was independent of pore size and depended only on porosity.