The Duke of Cambridge's jet touched down at Ben Gurion International Airport in Tel Aviv last night following William's packed two days in Jordan.
The prince's trip was announced in March and welcomed by Israeli and Palestinian officials.
The visit by the second in line to the British throne has been billed as a chance to bond with Hussein, a fellow graduate of Britain's Royal Sandhurst Military Academy.
For the 36-year-old William, second in line to the throne, it marks a high-profile visit that could brandish his global credentials.
The duke's visit comes during a period of increased tension in the region.
Later in the day, the prince will see Prime Minister Benjamin Netanyahu and President Reuven Rivlin before heading to Jaffa and Tel Aviv on the Mediterranean coast to meet young people participating in a football-based youth programme.
Yad Vashem chair Avner Shalev is guiding Prince William through the memorial's exhibitions detailing the death of six million Jews systematically killed by Nazi Germany and its collaborators during World War II.
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The Duke will be joined by Chief Rabbi Ephraim Mirvis during his visit, when he will leave his floral tribute in Yad Vashem's Hall of Remembrance.
Britain captured Palestine from the Ottoman empire in 1917 during World War One and administered the territory under global mandate until 1948, pulling out a day before Israel declared independence.
A spokesman for the prince, acknowledging the "well-known" and "complex challenges" in the Middle East, said William's tour, like other visits overseas by members of the British royal family, will be non-political.
The children greeted the two princes in the amphitheater of Jerash, where they showed him some of their art work, including paintings.
William, an avid soccer fan, arrived in Jordan on Sunday afternoon, at a time when the England-Panama World Cup game was under way. On Monday, June 25, William visited the archaeological site of Jerash in Jordan, where Kate at age four posed for a photo with her younger sister Pippa Middleton and their father Michael.
"I said to his Royal Highness that this is a unique opportunity for me to express my thanks to the British people for opening their homes to me and to the other 10,000 children who came", Alexander said.