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Stephanandra incisa is a typical discontinuous distribution species in the eastern part of the subspecies with a high economic and ecological value. In this study, we have obtained the complete chloroplast genome of S. incisa using high-throughput sequencing. The chloroplast genome length was 159,583 bp, the AT content was 63.7%, while the large single copy and a small single copy area were 88,018 bp and 18,817 bp, respectively. It contains 131 genes, including 86 protein-coding genes, 37 transfer RNA genes, and eight ribosomal RNA genes. A maximum-likelihood phylogenetic tree supported the fact that S. incisa is closely related to Pyracantha fortuneana and Amelanchier sinica, which is consistent with the taxonomic view.