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Gentiana apiata N. E. Br., is a perennial medicinal plant in the family Gentianaceae, which is recorded as near-threatened (NT) species in the Red List and endemic species only distributed in Qinba Mountain, China. The complete chloroplast genome sequence of G. apiata was sequenced using the Illumina Hiseq 4000 platform. The size of the G. apiata chloroplast genome is 151,069 bp, with an average GC content of 37.6%. This circular molecule has a typical quadripartite structure containing a large single-copy (LSC) region of 83,023 bp, a small single-copy (SSC) region of 17,256 bp, and two inverted (IRs) repeat regions of 25,395 bp. A total of 134 genes were successfully annotated containing 86 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 3 pseudogenes (rps19, ycf1, infA). A maximum likelihood (ML) phylogenetic tree supported the fact that the chloroplast genome of G. apiata is closely related to that of Gentiana hexaphylla.