Clinostomum complanatum is an important trematode in fishes, birds of the family Ardeidae, and humans. Until now, limited knowledge is available regarding its molecular epidemiology, ecology, and phylogenetic study. Knowledge of the full mitochondrial genome of C. complanatum will provide important information for the study of epidemiology, biology, and genetic diversity of this fluke. In the present study, the complete mitochondrial genome of C. complanatum was sequenced and analyzed. The complete C. complanatum mitochondrial genome is 13,796 bp in length and contains 12 protein-coding genes, 22 tRNA genes, two rRNA genes, and one non-coding control region. All the 12 protein-coding genes are transcribed in the same direction and are AT-rich. Phylogenetic analysis based on concatenated amino acid sequences of the 12 protein-coding genes from C. complanatum and other selective digeneans showed that C. complanatum is in a separate branch, indicating C. complanatum has no closer relationship with any of the selected families. The complete mtDNA sequence of C. complanatum will increase our knowledge of mitochondrial genomics data and will also provide an important resource for studies of inter- and intra-species variation of flukes belonging to Clinostomidae.