A stacked die package for an electromechanical resonator system includes a chip that contains an electromechanical resonator bonded onto the control chip for the electromechanical resonator by a thermally and/or electrically conductive epoxy. In various embodiments, the electromechanical resonator can be a micro-electromechanical system (MEMS) resonator or a nano-electromechanical system (NEMS) resonator. Packaging configurations that may include the chip that contains the electromechanical resonator and the control chip include chip-on-lead (COL), chip-on-paddle (COP), and chip-on-tape (COT) packages. The stacked die package provides small package footprint and/or low package thickness, as well as low thermal resistance and a robust conductive path between the chip that contains the electromechanical resonator and the control chip.