Rumex japonicus is a medicinal plant distributed in East Asia. Here, we report and characterize the complete plastid genome sequence of R. japonicus and size is 159,292 bp in length and contains the typical structure and gene content of other angiosperm plastomes, including two inverted repeat regions of 30,629 bp, a large single-copy region of 85,028 bp and a small single-copy region of 13,006 bp. There are 112 unique genes, including 78 protein-coding, 30 tRNAs and 4 rRNAs. We constructed a phylogenetic tree with 14 species and the phylogenetic topologies showed that R. japonicus was closely related to Rheum wittrockii.