His arrival was confirmed by airport sources and the head of his private office.
Prince Mohammed is set to hold talks with President Sisi, a key regional ally, and other officials in Egypt over his three-day visit, before flying off to the UK on Wednesday and then the United States.
Additionally, bin Salman will visit the Cathedral of St.Mark in Abbasiya where he will meet with Pope Tawadros II.
Both leaders discussed stepping up cooperation between Egypt and Saudi Arabia across all fields, and continued consultation and coordination on various regional and worldwide issues to enhance joint Arab action.
Authorities in Riyadh have taken an active interest in Egyptian politics following the overthrow of president Mohamed Morsi in 2013.
Mohammed bin Salman, 33, was greeted by Egyptian President Abdel Fattah el-Sisi as he disembarked from the plane on Sunday.
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Opposition to the deal has been a problem for Sisi, sparking the only major street protests since he came to power backed by Saudi in 2014 and becoming a rallying point for opposition figures that have been marginalized during his rule.
The crown prince has visited Egypt several times in recent years while serving as deputy crown prince.
The day before Prince Mohammed's visit, Egypt's top court dismissed all outstanding legal challenges to the deal on the Red Sea islands.
Last June, Egypt joined Saudi Arabia, the United Arab Emirates and Bahrain in a blockade against Qatar, accusing the oil-rich state of supporting terrorism, interfering in internal affairs and seeking closer ties with Iran, the arch-Saudi rival in the Gulf region.
In April 2016, the Custodian of the Two Holy Mosques, King Salman bin Abdulaziz paid Al-Azhar Mosque a visit, and put the foundation stones of its new city where Al Azhar University's students from all over the world reside.
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