Ephedra sinica has been utilized by humans for over 5000 years as Chinese herbal medicine in China. In this study, we reported the complete chloroplast genome of E. sinica. The chloroplast genome of E. sinica is 109,550 bp in length as the circular, which harbors a large single-copy (LSC) region of 59,962 bp, a small single-copy (SSC) region of 8106 bp and separated by a pair of inverted-repeat (IR) regions of 20,742 bp each. The overall nucleotide content of the chloroplast genome: A of 31.2%, T of 32.1%, C of 18.4% G of 18.3%, and 36.7% GC content. This chloroplast genome contains 118 genes, which includes 74 protein-coding genes (PCGs), 36 transfer RNA (tRNAs) and 8 ribosome RNA (rRNAs). Phylogenetic analysis result showed that E. sinica was most closely related to Ephedra equisetina in the family Ephedraceae using the Neighbor-Joining (NJ) method.