Endogenous bornavirus-like nucleoprotein elements (EBLNs) are sequences derived from bornaviral N genes in vertebrate genomes. Some EBLNs have been suggested to encode functional proteins in host cells; however, little is known about their evolution and functional relationship to the viral genes from which EBLNs originate. Here, we predicted functionality of EBLNs based on the properties of N as an RNA-binding protein. We showed an EBLN in miniopterid bats (miEBLN-1) has evolved under purifying selection and encodes an RNA-binding protein (miEBLN-1p) with biochemical properties similar to bornaviral N. Furthermore, we revealed miEBLN-1p interacts with host RNA-binding proteins, such as MOV10. These data suggest that miEBLN-1p has been exapted as an RNA-binding protein with similar properties to exogenous bornaviral N in miniopterid bats.