The Clausena lansium, originally native to the southern part of China and has a long history of cultivation, is a tree member of the family Rutaceae. Chloroplast genome sequences play a significant role in the development of molecular markers in plant phylogenetic and population genetic studies. In this study, we report the complete chloroplast genome sequence of C. lansium for the first time (accession number of MH047377). The chloroplast genome is 159,284 bp long and includes 113 genes. It's LSC, SSC, and IR regions are 88,634, 18,896, and 25,877 bp long, respectively. Phylogenetic tree analysis exhibited that C. lansium was clustered with other Rutaceae species with high bootstrap values.