The identity of the defendants remained under a gag order, Xinhua reported.
According to the details that were cleared for publication, one of them is a 29-year-old settler from the settlement of Adam in the occupied West Bank, and the others are 16-year-old minors from Jerusalem and Beit Shemesh, a suburb of Jerusalem.
The Jerusalem district attorney indicted the three on charges of kidnapping and murdering Abu Khedir from Shuafat, a Palestinian neighbourhood of Jerusalem, as well as other assaults and attempted assaults against Arabs.
Enraged by the murder of three Israeli teenagers who were abducted a few weeks earlier from the West Bank, the defendants July 2 went on "a manhunt that lasted several hours, during which they kidnapped and brutally murdered a child only because he was an Arab", the indictment said.
They strangled Abu Khedir and beat him on his head, and while he was unconscious they burnt him alive, according to the indictment.
The suspects planned the attack in advance and purchased materials, including gasoline and cable ties, prior to the murder.
According to the indictment, the initial target was a seven-year-old Palestinian child. The night before the murder, the defendants went looking for Arabs in another "trip of revenge", during which they attempted to kidnap Musa Zaloom of East Jerusalem, beating him and his mother who was walking with him and pushing another child in a stroller.
They also attempted to torch several vehicles in the Palestinian neighbourhood of Zur Baher.
"The indictment details a horrific act, perpetrated on a racist background," Israel's Attorney General Yehuda Weinstein said in a statement, adding that it was a "horrific crime" against an innocent youth, and expressed his "deep regret over this cruel act which violates basic human morality".
The three were indicted for kidnapping & murdering Abu Khedir, 16
The brutal killing triggered days of violent demonstrations during which masked Palestinians hurled stones at the police, who responded with tear gas and rubber-coated bullets. The protests began in Jerusalem and spilled over to some 10 towns and cities across Israel.