Stacked semiconductor die assemblies with heat sinks and associated methods and systems are disclosed. In some embodiments, a controller carrying one or more memory dies may be attached to a front side of a substrate. The substrate may include a heat sink formed on its back side such that the heat sink can establish a thermal contact with the controller. Further, the heat sink may be coupled to a thermally conductive pad of a printed circuit board (PCB) that carries the substrate. In this manner, the controller may be provided with a heat path toward the PCB to dissipate thermal energy generated during operation. In some cases, the substrate may include a set of thermal vias extending from the heat sink toward the controller to enhance the thermal contact between the controller and the heat sink.