Observing the spontaneous translocation of cell-penetrating peptides across a lipid bilayer in molecular dynamics simulations is challenging. However, in this study, we have successfully demonstrated the spontaneous translocation of Arg9 (nona-arginine) across a model membrane (DOPC/DOPG(4:1)) using the weighted ensemble method, which is known to be one of the most efficient transition path sampling methods. Our findings reveal a strong correlation between the movement of Arg9 and the water flow, and we have also observed that the tilt angle of Arg9 with respect to the membrane surface impacts the translocation. We anticipate that the weighted ensemble method can effectively observe the spontaneous translocation of various cell-penetrating peptides, leading to a better understanding of their transport mechanisms.