His two previous convictions were overturned. Woodfox has long maintained his innocence in that death in 1972, when inmates were protesting conditions inside the Louisiana State Penitentiary.
Louisiana Attorney General Buddy Caldwell is appealing the judge's order, saying Woodfox is a killer who should remain locked up.
The appeals court order blocks the release of Woodfox until at least Friday.
Woodfox and Herman Wallace were accused in the 1972 killing of guard Brent Miller at the Louisiana State Penitentiary at Angola. A third inmate, Robert King, was linked to Miller's death but never charged.
The group became known as the "Angola 3," and the case has been a cause celebre for years, with activists arguing there is no evidence tying the three men to the crime and decrying the decades they each spent in solitary confinement.
Woodfox -- who was originally imprisoned on an armed robbery conviction has said he had tried to point out injustices at the prison, including instances of segregation, corruption and rape, and was targeted and wrongfully accused because of his activism as a Black Panther.
King was freed after his conviction in the killing of a fellow inmate was overturned in 2001.
The same went for Herman Wallace, who was released in 2013 after a judge vacated his murder conviction and sentence. He only experienced a few days of freedom; he was suffering from terminal liver cancer and died just days later.
A federal appeals court overturned Woodfox's conviction last year. But he has remained behind bars and is awaiting a third trial.
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