A jury was unable to reach a verdict on allegations that his actions led to the deaths of 95 Liverpool fans at a trial held at Preston Crown Court earlier this year.
Sitting at the same court, Sir Peter Openshaw ruled on Tuesday that he must face a retrial.
“I authorise a retrial of defendant David Duckenfield,” he told the hearing, which was attended by victims’ relatives.
The 74-year-old denied the charges but the Crown Prosecution Service sought a retrial after a jury was discharged in April following a 10-week trial.
The application was resisted by lawyers for Mr Duckenfield, a retired South Yorkshire Police chief superintendent.
The retrial is expected to start on 7 October.
Ninety-six men, women and children died in the crush on the Leppings Lane terrace at the FA Cup semi-final on 15 April 1989.
There can be no prosecution over the death of the 96th victim, Tony Bland, under the law at the time as he died more than a year and a day after his injuries were caused.
The crush unfolded the Hillsborough stadium in Sheffield, which had been chosen as a neutral venue to host the 1989 FA Cup semi-final between Liverpool and Nottingham Forest.
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