Here, we report the complete mitochondrial genome sequence of Gephyrocharax atracaudatus. The genome is found to be 17,049 bp in length and has a base composition of A (29.95%), G (15.29%), C (26.13%) and T (28.63%). Similar to other Gephyrocharax species, it contains a typically conserved structure including 13 protein-coding genes, 2 rRNA genes, 1 control region (D-loop) and 22tRNA genes. The proportion of coding sequences with a total length of 11,420 bp is 66.98%, which encodes 3800 amino acids. All protein-coding genes started with Met, ND1, ND2, ND3, ND4L, ND5 and CytB ended by TAA as a stop codon, CO1 ended by AGG as a stop codon, CO2, ATP6, ND4 ended by a single T, ATP8, ND5 ended by TAG as a stop codon and CO3 ended by TA as a stop codon. The lengths of 12S ribosomal RNA and 16S ribosomal RNA are 950 bp and 1682 bp, respectively. The length of control region is 1396 bp, ranging from 15,653 bp to 17,049 bp. The complete mitochondrial genome sequence provided here would be useful for further understanding the evolution of ratite and conservation genetics of Gephyrocharax atracaudatus.