The late-time evolution of the neutrino event rate from supernovae is evaluated for Super-Kamiokande using simulated results of proto-neutron star (PNS) cooling. In the present work we extend the result of Suwa et al. (2019) [arXiv:1904.09996], which studied the dependence on the PNS mass, but focus on the impact of the nuclear equation of state (EOS). We find that the neutrino event rate depends on both the high-density and low-density EOS, where the former determines the radius of the PNS and the latter affects its surface temperature. Based on the present evaluation of the neutrino event rate we propose a new analysis method to extract the time variability of the neutrino average energy taking into account the statistical error in the observation.