Ruto is accused along with Kenyan President Uhuru Kenyatta of helping to orchestrate post-election violence five years ago in which 1,200 people died. He had asked for the trial to be held in Kenya or neighbouring Tanzania, where there is already a U.N. court.
"While in principle in favour of bringing the ICC's proceedings closer to the affected communities, (judges) concluded that the proceedings in this instance shall be held at the ICC's headquarters," the court said in a statement.
It has yet to rule on a similar request by Kenyatta. The two men, who were elected on a joint ticket in March, had asked for the move so that they could more easily combine their political duties with attending court. Critics said it might expose prosecution witnesses to intimidation.
The court said judges had considered factors including "the potential impact on victims and witnesses" and the "perception of the court". Their decision will be controversial in Kenya and Africa more broadly, where sensitivities about European and Western influence run deep.
Earlier this year, heads of state and government at an African Union summit urged the ICC to refer the charges against Kenyatta and Ruto back to the Kenyan courts.