Jason Greenblatt's visit comes after more than a week of tensions over the Haram al-Sharif mosque compound, known to Jews as the Temple Mount and central to the Israeli- Palestinian conflict.
Israel installed metal detectors at entrances to the site, which includes Al-Aqsa mosque and the Dome of the Rock, following an attack on July 14 that killed two policemen.
Palestinians view the move as Israel asserting further control over the site. They have refused to enter the compound in protest and have prayed in the streets outside.
Clashes have broken out during protests over the measures, leaving five Palestinians dead.
On Friday, a Palestinian broke into a home in a Jewish settlement in the occupied West Bank and stabbed three Israelis to death.
An incident last night in Amman that, according to Israeli officials, saw a Jordanian attack an Israeli security guard with a screwdriver at the Israeli embassy compound raised further concerns, though it was not immediately clear if there was any link.
Separately today, Israeli tank fire struck a Hamas post in the Gaza Strip after what was believed to be a rocket from the enclave landed in an open area in Israel.
With fears further unrest could follow, Greenblatt "departed for Israel last night to support efforts to reduce tensions in the region," a US official said on condition of anonymity.
The UN Security Council will also hold closed-door talks today about the spiralling violence after Egypt, France and Sweden sought a meeting to "urgently discuss how calls for de-escalation in Jerusalem can be supported".
"Since the start of the events, I have held a series of assessments with security elements including those in the field," Israeli Prime Minister Benjamin Netanyahu said Sunday.
"We are receiving from them an up-to-date picture of the situation, as well as recommendations for action, and we will decide accordingly."
Arab League chief Ahmed Abul Gheit on Sunday accused Israel of "playing with fire" with the new security measures, and Turkish President Recep Tayyip Erdogan called them an insult to the Muslim world.
Friday's main weekly Muslim prayers - which typically draw thousands to Al-Aqsa - brought the situation to a boil.
In anticipation of protests, Israel barred men under 50 from entering the Old City for prayers.
Clashes broke out between Israeli security forces and Palestinians around the Old City, in other parts of annexed east Jerusalem and in the occupied West Bank, leaving three Palestinians dead.
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