Folium isatidis is a native Chinese herbaceous plant widely used for medicinal purposes for thousands of years. However, few studies have focused on the leaves of Isatis indigotica. In this report, we isolated a series of four fractions (I-IV) from Folium isatidis and explored the antiviral activity of each tested extract. The extracts were active against a panel of RNA and DNA viruses in vitro, namely influenza A virus (IAV), coxsackie virus B3 (CVB3), respiratory syncytial virus (RSV), and adenovirus type 7 (Ad-7). Oral administration of 200 mg/kg/d of fraction III in mice exerted strong antiviral effects in viral replication, accompanied by prolonged survival rate, attenuated lung tissue damage as well as significant reductions in pulmonary virus titers and lung index. Our results provide the first biochemical evidence that Folium isatidis and its extracts could be used as potential antiviral agent in the postexposure prophylaxis for multiple viral infections.