We present here the first complete genome sequence of Helicobacter pylori strain GD63, isolated from a 72-year-old male Vietnamese patient with a chronic gastric ulcer. The genome consists of a 1.6-Mbp chromosome and an 8.9-kbp plasmid. The strain is cag pathogenicity island (cagPAI) and VacA positive and belongs to the hpEAsia lineage.