High thermal performance microelectronic modules containing thermal extension levels are provided, as are methods for fabricating such microelectronic modules. In various embodiments, the microelectronic module includes a module substrate having a substrate frontside and a substrate backside. At least one a microelectronic device, such as a semiconductor die bearing radio frequency circuitry, is mounted to the substrate frontside. A substrate-embedded heat spreader, which is thermally coupled to the microelectronic device, is at least partially contained within the module substrate, and extends to the substrate backside. A thermal extension level is located adjacent the substrate backside and extends away from the substrate backside to terminate at a module mount plane. The thermal extension level contains a heat spreader extension, which is bonded to and in thermal communication with the substrate-embedded heat spreader.