Atractylodes japonica Koidz. ex. Kitam. (Asteraceae) is a perennial plant, of which the dried rhizome has been utilized as a traditional herbal medicine in East Asia. Here, we sequenced and annotated the complete chloroplast genome of A. japonica native to Korea. The circular genome was 153,207 bp in length and was composed of a large single-copy region (84,256 bp), a small single-copy region (18,657 bp), and a pair of inverted repeat regions (25,147 bp each). The annotation and manual curation of genes predicted a total of 114 genes, of which 80 were classified as protein-coding genes, 30 were transfer ribonucleic acid (RNA) genes, and 4 were ribosomal RNA genes. Phylogenetic analysis using 13 genomes from 6 Atractylodes species showed intermingled clustering of 9 genomes from 4 species, A. chinensis, A. japonica, A. koreana, and A. lancea, indicating ambiguity in their taxonomic identification.