Shoukry, who arrived here to discussan Egyptian initiative to break the deadlock, said his trip was a "continuation of Egypt's longstanding sense of responsibility" towards peace for itself and all the people of the region.
Shoukry's visit marks the first by an Egyptian foreign minister in nine years.
Netanyahu welcomed the Egyptian initiative. "I welcome President al-Sisi's recent offer of Egyptian leadership in efforts to advance peace with the Palestinians and a broader peace in our region," he said.
Emphasising that Egypt was keen to promote peace, Shoukry thanked the two sides for showing faith in Cairo.
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"Today is a continuation of Egypt's longstanding sense of responsibility towards peace for itself and all the people of the region, particularly the Palestinians and the Israeli people, who have suffered for many decades due to the perpetuation of the conflict between them," Shoukry said.
"Such a monumental achievement would have far-reaching, dramatic and positive impact on the overall conditions in the Middle East region... Egypt remains ready to contribute towards achieving this goal. We greatly value the trust of both sides and the international community in our commitment to peace, stability and justice," Shoukry emphasised.
A spokesperson of the Egyptian Ministry of Foreign Affairs, Ahmed Abu Zeid, earlier said Shoukry and Netanyahu "will be to discussing the understandings that have already been reached, they will solidify trust between Israel and the Palestinians and renew negotiations, in an effort to arrive at a comprehensive and just solution to the conflict."
Netanyahu earlier made an announcement regarding the historic visit at the weekly cabinet meeting in the morning.
"The visit today is important in many ways," he said adding,"It shows the change in relations between Israel and Egypt, including [Egyptian President Abdel-Fattah] el-Sissi'si important call to advance the peace process both with the Palestinians and with Arab states."
The last time an Egyptian foreign minister visited Israel was in 2007.
Shoukry last month met Palestinian Authority officials in Ramallah and is said to have gained their support on the initiative.
Egypt became the first Arab state to sign a peace treaty with Israel in 1979.
Bilateral ties seems to have warmed up since el-Sissi came to power in Egypt in 2013 with Cairo sending a new Ambassador to Tel Aviv in early 2016.
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."
Peace talks between the two sides have largely remained frozen since Netanyahu came to power in 2009.