Sinowilsonia henryi Hemsl. (Hamamelidaceae) is a living fossil and an endangered relict species endemic to China. The complete chloroplast (cp) genome was sequenced and assembled by using Illumina paired-end reads data. The circular chloroplast genome consists of 158,741 bp, including a pair of inverted repeat (IR) regions of 26,233 bp each, a large single copy (LSC) region of 87,507 bp and a small single copy (SSC) region of 18,768 bp. The nucleotides consists of 30.5% A, 19.5% C, 18.7% G and 31.3% T. In total, the genome contained 135 genes, of which 87 are protein-coding genes (80 unique), 40 transfer RNAs (33 unique), and 8 ribosomal RNAs (4 unique). Phylogenetic analysis based on chloroplast genome sequences shows that S. henryi is closely related to Liquidambar formosana Hance.