Fannia pusio, the chicken dung fly species, remains unexplored despite its forensic, sanitary, and veterinary importance in the Nearctic and Neotropical regions. In this study, we obtained the complete mitochondrial genome of Fannia pusio for the first time using next-generation sequencing. We compared it with the previously published mitogenomes of the genus from the Palearctic region, and its phylogenetic position was studied based on the concatenated protein-coding genes (PCGs) dataset of Calyptratae flies. The circular mitochondrial genome of F. pusio is 16,176 bp in length, with a high A+T content (78.3%), whose gene synteny, codon usage analysis, and amino acid frequency are like other previously reported Fannia species. All PCGs underwent purifying selection except the nad2 gene. Interspecific K2P distances of PCGs of Fannia yielded an average of 12.4% (8.1% to 21.1%). The Fannia genus is supported as monophyletic, including the neotropical Fannia pusio and the remaining species from the Palearctic region. Further taxonomic sampling, including members of the other genera, is needed to deep into the phylogenetic relationships of this species group. These results provide a valuable dataset for studying the mitochondrial genome evolution and a resource for the taxonomy and systematics of Fanniidae.