Feline panleukopenia is a common contagious disease with high morbidity and mortality. At present, feline parvovirus (FPV) and canine parvovirus (CPV) variants are the pathogens of feline panleukopenia. Many studies have shown that miRNAs are involved in virus-host interactions. Nevertheless, miRNA expression profiling of FPV (original virus) or CPV-2b (new virus) in cats has not been reported. To investigate these profiles, three 10-week-old cats were orally inoculated with 106 TCID50 of the viruses (FPV and CPV-2b), and the jejunums of one cat in each group were sectioned for miRNA sequencing at 5 days post-inoculation (dpi). This study is the first attempt to use miRNA analysis to understand the molecular basis of FPV and CPV infection in cats. The miRNA expression profiles of the jejunums of cats infected with FPV and CPV were obtained, and a subset of miRNAs was validated by real-time qPCR. The results show that a variety of metabolism-related pathways, cytokine- and pathogen-host interaction-related pathways, and pathology- and cellar structure-related pathways, as well as others, were affected. Specifically, the JAK-STAT signaling pathway, which is critical for cytokines and growth factors, was enriched. This description of the miRNAs involved in regulating FPV and CPV infection in vivo provides further insight into the mechanisms of viral infection and adaptation and might provide an alternative antiviral strategy for disease control and prevention.