Polygala japonica Houtt. (Polygalaceae) is a perennial herbaceous plant widely distributed in south China. Here, we assembled and characterized the complete chloroplast (cp) genome of P. japonica using sequencing data. The complete cp genome of P. japonica was 165,439 bp in length, with a GC content of 36.7%. The complete cp genome shows a typical quadripartite structure with a pair of inverted repeats (IRs) of 36,786 bp, separated by a large single copy region (LSC) of 83,722 bp, and a small single copy region (SSC) of 8,145 bp. A total of 135 genes were annotated in the cp genome of P. japonica , consisting of 89 protein-coding genes, 8 rRNA genes, and 38 tRNA genes. The phylogenetic analysis showed P. japonica had a closer relationship with P. tenuifolia.