It rejected claims by Mr Bargouti, a leader of the intifada, that Israel's justice system had no jurisdiction over him.
"
The state of Israel doesn't have the right to try me or accuse me
"
Marwan Barghouti
Mr Barghouti has argued that Israel cannot try him because he is an elected member of the Palestinian parliament, and because he says he was detained illegally by soldiers.
He denies Israel's accusations that he was involved in attacks that killed 26 Israelis.
Judge Sarah Sirota told Mr Barghouti: "We have decided when to begin hearing testimony, from the morning of 6 April."
The three-judge panel did not immediately give reasons for the ruling.
But Mr Barghouti again said he did not recognise the court's power.
"The state of Israel doesn't have the right to try me or accuse me," he said.
"I am fighting for the rights of my people against the cruel occupation."
The court decided to appoint a public defender for Mr Barghouti, who has refused legal representation.
'Dismiss charges'
The trial began last October, but it has mostly consisted of pre-trial motions.
Mr Barghouti is the leader of Yasser Arafat's Fatah movement in the West Bank and is closely identified with its militant offshoot, the al-Aqsa Martyrs' Brigade.
He has been a popular face of the Palestinian uprising - or intifada - and is seen as a possible successor to Mr Arafat.
He says Palestinians have the right to use force in resisting Israeli occupation of the West Bank and Gaza Strip.
At the same time, he has given his backing to an eventual peace agreement that would allow a Palestinian state to exist alongside Israel.