Coronaviruses cause a wide range of diseases, ranging from the common cold to severe illnesses such as COVID-19. Although vaccines and therapeutics against COVID-19 have been developed, recent reports have documented the emergence of viral variants with reduced susceptibility to these interventions, suggesting that coronaviruses may continue to circulate persistently, similar to influenza viruses. Cirsium japonicum var. spinossimum Kitam. (hereafter referred to as C. japonicum) has traditionally been used to treat various medical conditions, including inflammatory diseases; however, its antiviral properties remain poorly understood. In this study, we demonstrated that C. japonicum extract inhibited human coronavirus replication and alleviated virus-induced cytotoxicity. Analysis of the chemical constituents of the extract identified cirsimaritin, a major flavonoid present in C. japonicum, as an active compound with antiviral activity against human coronavirus. The antiviral effects of both C. japonicum extract and cirsimaritin were further confirmed using scanning electron microscopy and a three-dimensional spheroid model. Finally, we demonstrated that C. japonicum extract and cirsimaritin inhibited coronavirus papain-like protease activity. These findings suggest that C. japonicum extract and cirsimaritin have potential as therapeutic candidates for coronavirus-associated diseases.