In this paper, we report the complete mitochondrial genome of an Australian little penguin (Eudyptula minor novaehollandia). The mitogenome sequence has been found to be circular, and 17,608 bp in length. Similar to other Spheniscidae species, the genome encoded a typically conserved structure consisting of 13 protein-coding genes (PCGs), two rRNA genes, and 22 tRNA genes, as well as all protein coding sequences started with methionine. The lengths of 12S ribosomal RNA and 16S ribosomal RNA were 977 bp and 1612 bp, respectively, and were located between tRNA-Phe and tRNA-Leu. The overall base composition of the mitogenome of E. minor novaehollandia had slightly higher AT (55.5%) content than GC (45.5%). The complete mitogenome sequence determined in this study would be useful to track the deeper evolutionary history and conservation of E. minor novaehollandia.