Pathogenic viral infections have become a serious public health issue worldwide. Viruses can infect all cell-based organisms and cause varying injuries and damage, resulting in diseases or even death. With the prevalence of highly pathogenic viruses, such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), it is urgent to develop efficient and safe approaches to inactivate pathogenic viruses. Traditional methods of inactivating pathogenic viruses are practical but have several limitations. Electromagnetic waves, with high penetration capacity, physical resonance, and non-contamination, have emerged as a potential strategy to inactivate pathogenic viruses and have attracted increasing attention. This paper reviews the recent literature on the effects of electromagnetic waves on pathogenic viruses and their mechanisms, as well as promising applications of electromagnetic waves to inactivate pathogenic viruses, to provide new ideas and methods for this inactivation.