Bretschneidera sinensis: Hemsl., a tree sparsely distributed in southern and southwestern China as well as northern Vietnam, is the only species of Bretschneideraceae. Being endangered in China, B. sinensis is one of the National Key Protected Wild Plants (Class I) and has been included in the China Plant Red Data Book. Here we reported its complete chloroplast genome sequence assembled from Illumina sequencing reads. The complete chloroplast genome was 159,004 bp long, consisting of a large single copy (LSC) region of 86,910 bp and a small single copy (SSC) region of 18,820 bp, separated by a pair of inverted repeat region (IRs) of 26,637 bp each. The chloroplast genome contained 132 genes, including 37 tRNA, 8 rRNA and 87 protein-coding genes. Phylogenetic analysis using the maximum likelihood method showed that B. sinensis is closest to Carica papaya among closely related species with available chloroplast genome sequences.