Oenanthe javanica (Bl.) DC. (Apiaceae) is a herbaceous species naturally distributed in China. The complete chloroplast genome sequence of Oenanthe javanica was generated by de novo assembly using whole genome next generation sequencing data. The chloroplast genome of Oenanthe javanica was 154,246 bp in length and divided into four distinct regions, such as large single copy region (84,142 bp), small single copy region (17,238 bp) and a pair of inverted repeat regions (26,433 and 26,433 bp). The genome annotation predicted a total of 123 genes, including 85 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed that Oenanthe javanica is nested in Apiaceae tribe Oenantheae and has a close relationship to Cicuta virosa and Cryptotaenia japonica.