One new lycopodine-type alkaloid (1), one new natural product (2), and eight known analogs (3−10) were isolated from the whole plant of Lycopodium japonicum Thunb. The structures of 1−10 were determined based on extensive comprehensive spectroscopic analyses, including UV, IR, NMR, and HRESIMS. Moreover, the isolated alkaloids were evaluated for their neuroprotective activity against Hemin-induced HT22 cell damage. Notably, compounds 1 and 10 exhibited potential neuroprotective activities, with 21.45% and 20.55% increase in cell survival at 20 μM, respectively. Moreover, compounds 1 and 10 revealed their protective effects on Hemin-induced apoptosis in HT22 cells.