Parabreviscolex niepini is a recently described caryophyllidean monozoic tapeworm from schizothoracine fish on the Tibetan Plateau. In the present study, the complete mitochondrial genome of P. niepini is determined for the first time. The mitogenome is 15,034 bp in length with an A+T content of 59.6%, and consists of 12 protein-encoding genes, 22 tRNA genes, two rRNA genes, and two non-coding regions. The secondary structure of tRNAs exhibit the conventional cloverleaf structure, except for trnS1((AGN)) and trnR, which lack DHU arms. The anti-codon of trnS1((AGN)) in the mitogenome of P. niepini is TCT. The two major non-coding regions, 567 bp and 1428 bp in size, are located between trnL2 and cox2, trnG and cox3, respectively. The gene order of P. niepini shows a consistent pattern with other caryophyllideans. Phylogenetic analysis based on mitogenomic data indicates that P. niepini has a close evolutionary relationship with tapeworms Breviscolex orientalis and Atractolptocestus huronensis.