In China, the stripe-throated yuhina is mainly distributed in southwestern and the population is not abundant. In this study, we sequenced and characterized its complete mitochondrial genome. The complete mitochondrial of stripe-throated yuhina is 17,843 bp in length and contained 13 protein-coding genes, 2rRNA genes, 22 tRNA genes, and 2 control regions. The overall base composition of the mitogenome was 30.6% A, 14.1% G, 23.99% T, 31.31% C. All the genes in the stripe-throated yuhina mitogenome were encoded on the H-strand, except for the ND6 and eight tRNA genes that were transcribed from the L-strand.