Indirect detection of dark matter via its annihilation products is a key technique in the search for dark matter in the form of weakly interacting massive particles (WIMPs). Strong constraints exist on the annihilation of WIMPs to highly visible Standard Model final states such as photons or charged particles. In the case of s-wave annihilation, this typically eliminates thermal relic cross sections for dark matter of mass below \U0001d4aa(10) GeV . However, such limits typically neglect the possibility that dark matter may annihilate to assumed invisible or hard-to-detect final states, such as neutrinos. This is a difficult paradigm to probe due to the weak neutrino interaction cross section. Considering dark matter annihilation in the Galactic halo, we study the prospects for indirect detection using the Hyper-Kamiokande (HyperK) neutrino experiment, for dark matter of mass below 1 GeV . We undertake a dedicated simulation of the HyperK detector, which we benchmark against results from the similar Super-Kamiokande experiment and HyperK physics projections. We provide projections for the annihilation cross-sections that can be probed by HyperK for annihilation to muon or neutrino final states, and discuss uncertainties associated with the dark matter halo profile. For neutrino final states, we find that HyperK is sensitive to thermal annihilation cross-sections for dark matter with mass around 20 MeV, assuming an NFW halo profile. We also discuss the effects of neutron tagging, and prospects for improving the reach at low mass.