Israeli Prime Minister Benjamin Netanyahu calls the killing an act of terror.
Terror group Hamas hailed the group’s first military operation of the year, despite Israel’s charges the assassination was an act of terrorism.
The shooting came ahead of Netanyahu’s meeting in Turkey with Turkish President Recep Tayyip Erdogan.
Netanyahu said the man was transferred to Israel via a military checkpoint and was about to enter Israel.
The man was identified as Mohammed Abu Khdeir, a 16-year-old from East Jerusalem.
Israel’s top general in the West Bank, Maj. Gen. Yoav Mordechai, gave a first-hand account of the killing.
There are conflicting reports about the man’s identity, with Israeli officials saying he was an Arab.
Abu Khdeir was “executed in cold blood,” senior defense official Lt. Col. Peter Lerner said in a statement.
The operation began at 2:15 a.m. local time, or 4:15 p.m. Wednesday in the US Eastern time zone, said a statement from the military.
“The forces are advancing with, and are confronted by, Palestinian rioters who are throwing stones and firebombs,” the military said. “The forces use rubber bullets, live fire and stun grenades. They are making progress and have established a perimeter containing [the] terrorist assailant.”
Kitted out for a holiday
The teen’s body was taken to the Al-Aqsa Mosque compound in Jerusalem’s Old City, which is believed to be the holiest site in Judaism and Islam, according to The Jerusalem Post.
The youth was bundled into a black bag, sprayed with a liquid, shot in the head and left to bleed out in a parking lot, the newspaper reported. The assailant was then taken away, followed by Israeli soldiers and Palestinian security forces.
It’s an area known as The Temple Mount, according to a local Jerusalem resident, Edna Tala.
“This is the holiest place for us and for all Muslims. It’s very sad, and this happens every year,” Tala told CNN.
Watch CNN’s coverage of the shooting in Jerusalem
An Arab Israeli running across a road, and stabbing
One of the assailants, wearing a Palestinian kaffiyeh scarf, stabbed an Israeli woman, ages 48 and 18, and a 63-year-old Israeli civilian, Israeli media reported.
Four Israeli soldiers have been wounded in retaliatory attacks, the military said. There was an attempt to throw a hand grenade at Israeli forces, according to Lior Lahav, a spokesman for the Israel Defense Forces.
Israeli families line the streets as helicopters buzz overhead and the live broadcast of the firefight does not end. The exchanges continued through the day.
Israeli Prime Minister Benjamin Netanyahu: ‘Our enemies got what they deserve’
Turkish President Recep Tayyip Erdogan called on Israel to immediately extradite the assailant. “This murder must end immediately and any terrorist elements that remain should be contained,” Erdogan told reporters in Istanbul.
CNN could not independently verify the attackers identity.
Netanyahu responded to Erdogan’s comments Thursday morning in Jerusalem.
“So, the worst nightmare that Israel would have as a state of Israel for the rest of its life, as the sole defender of the values of democracy, human rights and peace in the region, is being realized today,” Netanyahu said.
“Our enemies got what they deserve,” he said, “and they will not succeed in thwarting Israel’s determination to protect its people.”