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We report the development of a nano-engineered cryogenic adhesive (nECA) consisting of an epoxy impregnated with single walled carbon nanotubes (SWNT) for bonding niobium-based superconductor multi-chip modules (MCMs). The nECA offers 300%-900% enhancement in thermal conduction over the base adhesive while maintaining high electrical resistivity. Additionally, we report the thermal modeling results for a niobium-based superconducting single chip module with the incorporation of pure epoxy and nECA. When the heat flow is exclusively through the In/Sn bumps the thermal model predicts >; 100 mK temperature difference between the flipped chip with active circuitry and the passive carrier substrate, which might degrade the chip's performance and the operating margins. With the use of 0.1 wt% SWNT loaded epoxy as the underfill, we report reduction of temperature differences to a more acceptable level of ~ 19 mK. These results are expanded to foreseeable MCM package designs to highlight the merit of nECA as an underfill material for superconducting electronic packages.