The new decision reopens a murky case that has dogged Kirchner since her presidency.
She is accused of conspiring to protect high-ranking Iranian officials suspected of ordering the Lebanese Shiite militant group Hezbollah to carry out the attack.
Kirchner, Argentina's president from 2007 to 2015, allegedly received oil and trade benefits from Iran in exchange for signing off on a deal that enabled the suspects to avoid prosecution.
The accusations were first leveled by the late prosecutor Alberto Nisman, who was found dead the night before he was due to present them to Congress in January 2015.
Iran has denied involvement in the attack. Kirchner likewise denies the allegations against her.
Four lower courts had thrown the case out on grounds there was no evidence a crime had been committed.
But the new decision reopens a murky case that has dogged Kirchner since her presidency, a day after she was charged in a separate corruption case.
The three judges also ordered the case be removed from the court of their colleague Daniel Rafecas and transferred to a randomly selected judge.
Rafecas threw out the original request to reopen Nisman's case, brought by the Delegation of Argentine Jewish Associations (DAIA).
The unsolved bombing at the Argentine Jewish Mutual Association (AMIA) in Buenos Aires was the deadliest terror attack in Argentine history.
It still haunts the country two decades later.
No one has been convicted for the bombing, which wounded 300 people.
Nisman's death also remains unsolved nearly two years on.
The case was transferred in September to federal investigators, who are now tasked with determining whether it was a suicide or homicide.
Nisman, who had ordered arrest warrants for Iranian officials, including ex-president Akbar Hashemi Rafsanjani, was found dead on his bathroom floor with a bullet through his head.