Egypt withdrew its ambassador shortly after the outbreak of the Palestinian intifada in September 2000, while Amman did not replace a departing envoy in protest at Israel's actions to quell the uprising.
The new Jordanian envoy will be Maaruf Bakhit, who has just wound up a posting as ambassador to Turkey.
"We hope he will be able to do his job in a manner to improve ties as well as help advance the peace process," Jordanian Foreign Minister Hani Mulki said this week.
Jordan's main objective is a two-state solution leading to the establishment of an independent Palestinian state living side by side a secure Israel, in line with the internationally drafted Middle East peace roadmap.
Following the election in January of moderate Mahmud Abbas as the new leader of the Palestinian Authority to replace the late Yasser Arafat, Jordan pledged to help push forward the Middle East peace process.
Israel and the Palestinians agreed on a cease-fire to put a lid on more than four years of deadly violence.
Bakhit is a retired army major general with a doctorate in political science who served as the head of a state committee that oversaw the implementation of the 1994 peace treaty between Jordan and Israel.
He is heading to Israel four months after the two neighbours marked the 10th anniversary of the peace treaty, with a pledge to remain committed to what they termed a "strategic" pact.