Recently, two genetically distinct influenza viruses were detected in bats in Guatemala and Peru. We conducted influenza A surveillance among four bat species in Egypt. Out of 1202 swabs, 105 were positive by RT-PCR. A virus was successfully isolated in eggs and propagated in MDCK cells in the presence of TPCK-treated trypsin. Genomic analysis revealed that the virus was phylogenetically distinct from all other influenza A viruses. Analysis of the HA gene suggested common ancestry with other H9 viruses and the virus showed low-level of cross-reactivity with sera raised against H9N2 viruses. Bats were seropositive for the isolated viruses. The virus replicated in the lungs of experimentally infected mice. While genetically distinct, this virus shares several avian influenza virus characteristics suggesting a more recent avian host origin.IMPORTANCE Through surveillance, we isolated and characterized an influenza A virus from Egyptian fruit bats. This virus had affinity to avian-like receptors but was also able to infect mice. Our findings indicate that bats may harbor a diversity of influenza A viruses. Such viruses may have the potential to cross the species barrier to infect other species including domestic birds and mammals and possibly humans.