Wednesday's decision in favor of Khalid Sheik Mohammed -- the alleged mastermind of the attacks -- and his co-defendants vacated a decision by the military panel handling the case, known as a Court of Military Commission Review, made in June. The now-vacated ruling in favor of the government reinstated two charges for Sheik and his co-defendants.
The US has held Mohammed in Guantanamo Bay prison for more than a decade.
At issue in Wednesday's decision was the question of bias for Judge Scott Silliman, who was a member of the panel that issued a decision on an appeal in June.
Mohammed's side argued Silliman was not an impartial arbiter, and pointed to comments Silliman made in 2010, calling Mohammad and the co-defendants "the major conspirators in the 9/11 attacks."
The DC court sided with Mohammed unanimously, saying Silliman should have recused himself from the case.
Wednesday's decision from a civilian court adds yet another delay to the military's winding and controversial case, which has gone on for years. Without a government appeal of this decision, the military will have to gather a new panel to hear the appeal again.
"That may not seem like much of a delay, but these delays add up," said Steve Vladeck, a CNN legal contributor who serves as a counsel of record on a related issue before the Supreme Court.
Further, Vladeck pointed out the case was still at an early stage in the process.
Maj. Ben Sakrisson, a Department of Defense spokesperson, told CNN: "The appeals court decision speaks for itself."
Prior to Wednesday's decision, the DC Appellate Circuit -- which has authority over the military commission -- has handed down two other decisions against the military process over the past three years.
Nearly two years after the 9/11 attacks, the US announced Mohammed's capture, and in 2006 he was transferred to the US military prison in Guantanamo Bay, Cuba. The US subjected Mohammed to torture during its interrogation, compounding the complexities of the government's legal case against him, and began the military case at the tail end of the Bush administration.
The Obama administration put the case on hold and attempted to move it to the civilian court system, before allowing the military commission to proceed.