Escherichia coli AA86 (=KACC 15541) is an enteric bacterium that was isolated from a sample of healthy cow feces. Its genome sequence revealed that it is most closely related to the human fecal strain E. coli SE15 and could be classified under E. coli phylogenetic group B2. Here, we report the genome sequence of E. coli AA86, consisting of 3 contigs and 2 plasmids.