Buddleja alternifolia is China’s specialty, and scattered in northwest China. Here, we assembled and characterized the complete chloroplast (cp) genome of B. alternifolia using Illumina sequencing data for the first time. The complete cp genome was 154,280 bp in length, consisting of a pair of inverted repeats of 25,440 bp, a large single-copy (LSC) region of 85,330 bp, and a small single-copy (SSC) region of 18,070 bp. The genome encoded 115 unique genes, including 80 protein-coding genes, 31 tRNA genes, and four rRNA genes. Phylogenetic analysis based on 16 complete cp genome sequences indicated that B. alternifolia is closely related to Buddleja colvilei.