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Gymnocarpos przewalskii (Caryophyllaceae) is a desert shrub, which is listed as an endangered species in the Red List of China. In this study, the complete chloroplast (cp) genome of G. przewalskii is reported. The genome size is 150,636 bp, with an average GC content of 36.5%, containing a pair of inverted repeat (IR, 25,350 bp) regions, separated by a large single copy (LSC, 83,114 bp) and a small single copy (SSC, 16,822 bp) region. There are 111 genes, including 77 protein coding genes, 30 tRNA genes and 4 rRNA genes. We also reconstructed the phylogeny of Caryophyllaceae based on all published cp genomes. The maximum likelihood (ML) trees supported Gymnocarpos as the basal taxon of Caryophyllaceae.