Elaeagnus pungens is an evergreen shrub with high medicinal values. In this study, the complete chloroplast (cp) genome of E. pungens was characterized. The chloroplast genome of E. pungens is 152,218 bp in length, consisting of two 25,876 bp inverted repeats, 18,231 bp small single copy region, and 82,235 bp large single copy region. The chloroplast genome contains 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenomic analysis revealed that E. pungens and species from Elaeagnus formed a monophyletic clade sister to the clade consisting of species from Hippophae.