Britain's Prince William, left, and Jordanian Crown Prince Hussein look at a photograph showing William's wife, the former Kate Middleton, her father Michael and younger sister Pippa in the ruins of the Roman city of Jerash in the 1980s.
In a statement to launch the trip Kensington Palace had said a day "in the Occupied Palestinian Territories will begin with a short briefing on the history and geography of Jerusalem's Old City from a viewing point at the Mount of Olives".
William, a 36-year-old grandson of Queen Elizabeth and second in line to the throne, will see religious sites, honor Holocaust victims and meet Jewish and Arab youths, and Israeli and Palestinian leaders.
"Welcome to Israel, a great historic visit".
British Foreign Office Minister Alistair Burt said the visit is an "important and unique opportunity to promote diplomatic and cultural ties in the region".
The visit comes just after Israel marked its 70th anniversary of independence and amid surges of violence along the Gaza border.
He was given a short tour of the museum before meeting two survivors of the Holocaust, in which six million Jews were murdered during World War II.More news: Uruguay join Russia in knockout stage as Egypt, Saudi Arabia crash out
In a 1994 visit to Yad Vashem, Prince Philip, the Duke of Edinburgh, planted a tree there in his mother's honor.
He will then meet with Palestinian Authority President Mahmoud Abbas in Ramallah in the West Bank on June 26.
Speaking before William's visit, Alexander, freshly back from a bicycle ride that retraced his life-saving voyage as a toddler, said he was chosen to meet the prince as the youngest member of the Kindertransport.
Israel captured east Jerusalem from Jordan in the 1967 Mideast war and annexed it in a move not internationally recognized.
Upon arrival, the British royal was welcomed by Jordan's Crown Prince Hussein. and it went beyond the formal setting. The pair later watched the England-Panama World Cup match together.
Yad Vashem's Chairman Avner Shalev will accompany Prince William who will participate in a memorial ceremony in the Hall of Remembrance, visit the Children's Memorial, and sign the Yad Vashem Guest Book.
The memorial has recognized Prince William's great-grandmother, Princess Alice, as Righteous Among the Nations for her role in rescuing Jews during the Holocaust.