Cyclophilins (Cyps) are a subgroup of peptidyl-prolyl cis-trans isomerases (PPIases) that contain a highly conserved domain of PPIases. Sixteen Cyps have been identified in humans, among which the functions of five classical Cyp subtypes (CypA, B, C, D, and 40) have been studied in more detail. Cyps are widely expressed in almost all human tissues and are involved in several intracellular signaling pathways such as oxidative stress, mitochondrial dysfunction, cell migration, and apoptosis. Several studies have also demonstrated that Cyps play an important role in the development of cardiovascular diseases, neurodegeneration, cancer, and other diseases. However, as regulators of intercellular communication, Cyps have increasingly attracted attention as a result of their implications in viral infection. The specific motifs of Cyps can be targeted by viral proteins and thus promote either a viral infection or an antiviral response. This review highlights the present understanding of Cyps in viral infection and immune response. These effects will facilitate revealing the molecular mechanisms of several diseases induced by viruses and may provide novel insight into the development of corresponding drug-based treatment methods.