In this paper, we report the genomic architecture of a complete mitogenome from a Wedge-tailed eagle (Aquila audax). The mitogenome sequence was circular, and 17,494 bp in length. Compared to other members of the family Accipitridae, the genome encoded a conserved structure consisting of 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, a repeat region and a control region (D-loop), with all protein-coding sequences started with methionine. The lengths of 12S and 16S ribosomal RNA were 971 bp and 1545 bp, respectively, and were located between tRNA-Phe and tRNA-Leu. The overall base composition of the mitogenome of A. audax was dominated by higher AT (54.3%) than GC (45.7%) content. The complete mitogenome sequence determined in this study would be useful to track the deeper evolutionary history and the conservation of A. audax.