This is the first visit in Israel by an Egyptian foreign minister in nine years.
Speaking at a news conference alongside Mr. Netanyahu on Sunday, Mr. Shoukry called for revived peace talks between Israel and Palestine, voicing support for the two-state solution, and promised Egypt's support for peace negotiations.
"During a joint press conference with the Israeli prime minister, Shoukry said his visit to Israel comes at a crucial and challenging juncture for the Middle East". The Palestinians say Israeli settlement expansion denies them a viable state they seek in the occupied West Bank, the Gaza Strip and a capital in Arab East Jerusalem.
"The goal that we aim to achieve through negotiations between the two parties is one that is based on justice, legitimate rights and mutual willingness to coexist peacefully in two neighboring independent states in peace and security", Mr. Shoukry said.
But while claiming to be in favour of the "general idea" of the Arab Peace Initiative, Netanyahu has made clear he would not accept it in its present form.
Shoukry also briefed his Jordanian counterpart Nasser Gouda over the results of his visit to Israel regarding peace talks.
In a speech in May, el-Sissi made an appeal to Israel and the Palestinians to seize the opportunity to make a historic peace agreement that would "bring stability to the Middle East".
However, relations cooled over Israel's policies towards the Palestinians, and were further soured after the June 2012 election of the Muslim Brotherhood's Mohamed Morsi as Egyptian president.
After Israel and Turkey ended a six-year rift last month and said they would start talks on energy supplies, Netanyahu publicly sent a message of reassurance to Sisi.
A spokesman for Netanyahu said that "as in all of the previous cases" of suspicions against the premier, "this will contain nothing too - because there's nothing there".
Earlier in June, Prime Minister Benjamin Netanyahu said Israel would be interested in an altered draft of the initiative.
Morsi was, himself deposed in July 2013 by then-army chief Abdel Fattah el-Sisi, who was elected Egypt's president in 2014.
At least 214 Palestinians, 34 Israelis, two Americans, an Eritrean and a Sudanese have been killed.
In May, Israel's state comptroller issued a report critical of the financial aspects of Netanyahu's foreign trips from 2003 to 2005, when he served as finance minister. "This cooperation with Egypt is a security and worldwide asset for the State of Israel".
Emmanuel Navon, a Tel Aviv University political scientist who studies Israel-Africa relations, said he was skeptical that Netanyahu's visit would lead African countries to change their United Nations voting patterns.