In this study, we sequenced the complete mitochondrial genome of the shield-faced leaf-nosed bat ( Hipposideros lylei Thomas, 1914) using the Illumina platform. The mitochondrial genome of H. lylei is 16,856 bp in length, encoding 37 genes, which include 13 protein-coding genes, 22 tRNA genes, two rRNA genes, one replication start, and one non-coding control region (D-loop) of 417 bp in length. It has a G + C content of 42.0%, lower than the A + T content, indicating an obvious AT base preference. Phylogenetic analyses revealed that H. lylei clusters with three species of the genus Hipposideros in one branch and is relatively closely related to H. armiger and H. larvatus .