In summary, our findings demonstrate that a clinically in-use antibacterial drug, fidaxomicin, potently inhibits ZIKV infection both in vitro and in vivo through directly targeting an essential ZIKV non-structural protein, NS5 RdRp, robustly alleviating neurologic lesions in the CNS caused by ZIKV and preventing infected mice from morbidity. Here, RAF1 is linked to Zika virus infectious disease.