The teenager, who was not named in the indictment on Thursday because he is a minor, was one of five students arrested after the death of Aisha al-Rawbi, 47, who died of a head wound in October after stones were thrown at her near an illegal Israeli settlement in the occupied West Bank.
Besides manslaughter, which carries a maximum sentence of 20 years, the prosecutors allege the teen threw the stone in the anti-Arab attack "as part of an act of terror". He was also charged with stone-throwing and intentional sabotage of a vehicle, both "under terrorist circumstances".
Al-Rawbi died after a 2kg stone smashed through the windshield of the car she was travelling in with her husband and nine-year-old daughter in the West Bank on October 12.
Her husband managed to continue driving and make it to a Palestinian clinic, where al-Rawbi eventually died, according to prosecutors.
Footage of the scene showed what appeared to be a blood-stained broken brick at the foot of the passenger seat, which was covered in shattered glass and bloodstains.
Al-Rawbi's husband Yacoub said he had no faith in Israeli justice and wanted a hearing in an international court.
"The Israeli police and intelligence both know who hit us leading to my wife's death but they charged one person only," he said.
"When they hit our car with stones they were more than four people," he told AFP news agency.
"I want all those who killed my wife to be tried in an international court."