The Emberiza pusilla is a common bunting with very wide geographical range. Here, the complete mitochondrial genome of E. pusilla (16,790 bp in length) has been analyzed for building the database. The results showed that it consisted of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region. The base composition of mtDNA was A (29.6%), G (14.8%), C (32.8%), and T (22.9%), so the percentage of A and T (52.5%) was slightly higher than G and C. All the genes in E. pusilla were distributed on the H-strand, except for the ND6 subunit gene and 10 tRNA genes, which were encoded on the L-strand.