The judges said there were "substantial grounds" to believe Duterte, 81, played a key role in the murders of 76 people and the attempted murder of two others as part of his so-called "war on drugs", which prosecutors say killed thousands of civilians in the Philippines.
"The available evidentiary material shows the existence of a common plan between Mr Duterte and his co-perpetrators to kill alleged criminals in the Philippines, including those perceived or alleged to be associated with drug use, sale or production, through violent crimes including murder," the court said on Thursday.
In pre-trial hearings, his lawyers argued that Duterte's public statements that he would stop drugs and criminality in the Philippines and would tell security forces to go out and kill criminals were just rhetoric, meant to instil fear.
In the Philippines, the office of President Ferdinand Marcos Jr issued a statement to say it respected the ruling and justice must be served.
"Both sides stand to benefit from this. Justice for the accused if he is innocent, or justice for the victims if their rights were indeed abused," the statement said.
The case will now be assigned to a trial chamber, which will start planning for a trial.
In previous cases, it has taken the ICC up to a year between the confirmation of charges and the opening of a trial.
Prosecutors have said Duterte created, funded and armed death squads to target and kill suspected narcotics peddlers and users when he was in power between 2016 and 2022.
He was arrested and taken to The Hague last March.
Duterte has long insisted he instructed police to kill only in self-defence and has always defended the crackdown.
Appeals judges at the court on Wednesday had dismissed a bid to throw out Duterte's trial and said the court had jurisdiction over the case.
Lawyers for the octogenarian former president have also tried to argue that Duterte was unfit to stand trial because of alleged cognitive decline.
But judges in the pre-trial procedure ruled the case could move forward. It is rare for international courts to find suspects, even elderly ones, wholly unfit for trial.
The ICC has never found a suspect unfit for trial despite several other defendants' petitions.
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