Acer miaotaiense (Sapindales: Aceraceae) is a rare and vulnerable tree species endemic to China’s Mts. Qinling and Mts. Bashan. In this study, its complete chloroplast genome was assembled and characterized from the high-throughput Illumina sequencing data. The circular genome is 156,595 bp long, and contains a pair of inverted repeat (IR) regions of 26,100 bp each, separated by a large single-copy (LSC) region of 86,327 bp and a small single-copy (SSC) region of 18,068 bp. It harbors 137 genes, including 89 protein-coding genes (80 PCG species), 40 tRNA genes (30 tRNA species) and eight rRNA genes (four rRNA species). Its nucleotide composition is asymmetric (30.69 % A, 19.32 % C, 18.57 % G & 31.42 % T) with an overall A+T content of 62.12 %. Phylogenetic analysis indicates that A. miaotaiense is closely related to the congeneric A. morrisonense and A. buergerianum, and strongly supports that Acer and Dipteronia are sister taxa.