Acer pentaphyllum is a critically endangered maple confined to the valley of Yalong River in Southwest China. The whole chloroplast genome of A. pentaphyllum was 156,862 bp in length with a typical quadripartite structure, containing a large single-copy (LSC) region of 85,292 bp, a small single-copy (SSC) region of 18,146 bp, and a pair of inverted repeat (IR) regions of 26,712 bp separated among them. Totally 137 unique genes were predicted, comprising 89 protein-coding genes, 39 tRNA genes, and 8 rRNA genes (4 rRNA types). The phylogenetic analysis showed that A. pentaphyllum was resolved as sister to the clade containing A. griseum and A. sino-oblongum. This study reported the first complete chloroplast genome sequences of A. pentaphyllum and reconstructed a phylogeny tree based on 16 Sapindaceae species, which may provide new insight into phylogenetic studies of Sapindaceae and further conservation strategies for A. pentaphyllum.