Cosmic-ray muons that penetrate the Super-Kamiokande detector generate hadron showers in water, producing unstable radioactive isotopes through spallation reactions. These isotopes are major background sources for neutrino observation at MeV scale and the search for rare events. Super-Kamiokande has started observation using ultra-pure water since 1996, while gadolinium was loaded with 0.011wt% in 2020 aiming for improvement of neutron detection and the first observation of diffuse supernova neutrino background. In this study, we measured $^9\mathrm{Li}$ isotope generated by the muon spallation. $^9\mathrm{Li}$ decays with a lifetime of 0.26 seconds and emit an electron and a neutron with a branching ratio of 50.8%. These pairs of an electron and a neutron are difficult to distinguish from the inverse beta decay reaction caused by an electron antineutrino, and therefore become major background for the diffuse supernova neutrino background searches. In the data analysis, we selected $^9\mathrm{Li}$ event candidates by searching for pairs of low energy events following cosmic-ray muons. Before the gadolinium loading, the Super-Kamiokande experiment had an energy threshold of 8MeV for the measurement of electrons emitted from $^9\mathrm{Li}$. The threshold was lowered to 4.5 MeV by the reduction of the accidental background by requiring a total 8 MeV $\gamma$ rays from neutron captures on gadolinium. In this article, we report the analysis method and the measured spectrum of electrons from $^9\mathrm{Li}$ candidates.