Prions are infective agents composed of abnormally folded prion proteins (PrP^Sc), which are pathogenic isoforms of normal cellular prion proteins (PrP^C) that cause incurable, transmissible, neurodegenerative conditions in mammals called prion diseases. The spread of PrP^Sc within a host is facilitated by the lymphoreticular system, which uptakes and propagates PrP^Sc in the periphery and transmits them to the central nervous system. Our previous study showed that poly-l-arginine (PLR), a cationic amino acid polymer, inhibits PrP^Sc accumulation in neuroblastoma cells with persistent prion infection (ScN2a). Here, we report the beneficial effect of PLR against prions. In the in vitro prion infection experiment, PLR efficiently reduced the titer of prions inoculated to infect cultured N2a cells. In animal experiments, PLR inhibited the accumulation of PrP^Sc in the spleens of mice intraperitoneally inoculated with prions during asymptomatic periods. Prophylactic administration of PLR significantly prolonged incubation periods in mice intraperitoneally infected with prions, mitigating vacuolation and astrogliosis, although PrP^Sc level was not dramatically reduced in the brain. However, PrP^Sc level was reduced and the marginal zone distortion associated with prion infection was prevented in spleens of mice that was intraperitoneally infected with prions and received PLR, even at the terminal stage. Expression of follicular dendritic cell (FDC)-M1 antigens, a marker of FDC activation, and the level of PrP^Sc colonized within the white pulp of the spleens, as well as co-localization of FDC-M1 antigens and PrP^Sc, were reduced in these mice during the course of disease, suggesting that PLR counteracts the ability of FDCs that support PrP^Sc propagation in the spleen. Overall, prophylactically administered PLR suppresses prions in vivo, presumably through cellular control of pathological processes that occur in the spleen and eventually delay prion spread to the brain. This study presents implications for modulating the progress of prion diseases acquired peripherally.