In the last decade, several works have focused on exploring the material and electrical properties of GeTe/Sb2Te3 superlattices (SLs), in particular because of some first device implementations demonstrating interesting performances such as fast switching speed, low energy consumption, and non-volatility. However, the switching mechanism in such SL-based devices remains under debate. In this work, we investigate the prototype GeTe/Sb2Te3 SLs to analyze fundamentally their electronic and thermal properties by ab initio methods. We find that the resistive contrast is small among the different phases of GeTe/Sb2Te3 because of a small electronic gap (about 0.1 eV) and a consequent semi-metallic-like behavior. At the same time, the out-of-plane lattice thermal conductivity is rather small, while varying up to four times among the different phases, from 0.11 to 0.45 W m−1 K−1, intimately related to the number of Van der Waals (VdW) gaps in a unit block. Such findings confirm the importance of the thermal improvement achievable in GeTe/Sb2Te3 superlattices devices, highlighting the impact of the material stacking and the role of VdW gaps on the thermal engineering of the phase-change memory cell.