The court's order for a retrial makes Hakamada only the sixth death row inmate to get a retrial in Japan's history of postwar criminal justice.
Four were acquitted in their retrials, while the fifth inmate's case is still pending.
“We finally tore down the wall of retrial,” said Katsuhiko Nishijima, head of the defense team.
“We will challenge the court decisions, as well as police and prosecutors that have denied our appeals so many times.”
Thursday's ruling underscores Japan's much-criticized closed interrogations, which rely heavily on self-confession. Hakamada had confessed in a closed interrogation that lasted 20 days.
“If ever there was a case that merits a retrial, this is it,” said Amnesty International in a statement, saying questions over Hakamada's conviction based on a forced confession and the use of evidence must be answered.
