If a fraction of the cold heavy dark matter is boosted to relativistic energies, it can be efficiently detected in direct detection experiments as well as higher threshold neutrino detectors. This talk will present the search for boosted dark matter in the Super-Kamiokande experiment. Using the large water Cherenkov detector and its two decades of data initially taken for neutrino oscillation, we derived new limits on the dark matter-nucleon interaction cross-section, which are the most stringent constraint on the hadronic coupling of sub-GeV dark matter so far.