In this study, the complete mitochondrial genome of the medicinal mushroom Cordyceps militaris (Ascomycota, Cordycipitaceae) was sequenced. This mitochondrial genome is 33,277 bp in length and consisted of 14 protein-coding genes, 2 ribosomal RNA subunits and 27 transfer RNAs. The overall nucleotide composition of is 36.98% A, 26.23% T, 15.21% G and 11.59% C, with an AT bias of 73.21%. The mtDNA of C. militaris contains a total of eight group-І introns of which total size is 11,052 bp in length and four of them are in the rnl gene. The mitochondrial genome of C. militaris presented here provides the complete genome information of C. militaris.