Background: Chimarrogale leander is a species of the family Soricidae and is mainly distributed in southern China. Methods: Here, a complete mitochondrial genome for C. leander was assembled via high-throughput sequencing technology. Results The results showed that the complete mitogenome of C. leander is 17,357 bp and includes 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one control region. The nucleotide composition is A: 33.1%, T: 31.5%, C: 22.5% and G: 12.9%. Through the phylogenetic analysis of complete mitochondrial genome, it is found that C. leander has a close genetic relationship with Nectogale elegans. Conclusions: The new mitogenome will hopefully prove useful for systematic analyses of genus Chimarrogale.