Within hours of arriving, the two countries signed a memorandum of understanding to activate a 60-billion Saudi riyal ($16 billion) investment fund.
They also signed agreements to continue cooperation in resolving political crises in the Middle East, and a commitment to environmental protection.
Prince Mohammed, the Saudi deputy prime minister and minister of defense, was greeted by El-Sisi as he landed at Cairo International Airport.
During meetings, the two sides reviewed “strategic bilateral relations and discussed developments in the region “especially issues related to security and stability” and “fighting terrorism,” Saudi Press Agency reported.
The Crown Prince’s visit to Egypt was his first since he became crown prince in June of last year.
“The Egyptian president reaffirmed that the security of the Gulf is an integral part of Egyptian national security,” Egypt’s presidential spokesman, Bassam Rady said.
"President El-Sisi expressed Egypt's keenness to enhance bilateral cooperation with Saudi Arabia in all fields, in a way that reflects the level of strategic partnership between the two countries", Rady said.
Rady also highlighted the significance of the visit's timing in light of the "great challenges currently taking place in the Middle East, which require mutual coordination between Egypt and Saudi Arabia."
Ahead of the visit, Egyptian Foreign Minister Sameh Shukri said the Crown Prince and El-Sisi would “discuss the political situation in Yemen, Syria, Lebanon, Iraq and Libya.”
Prince Mohammed will also meet Prime Minister Sharif Ismail, the parliament speaker Ali Abdel-Aal, the grand Sheikh of Al-Azhar, Ahmed Tayeb and Pope Tawadros, the head of the Egyptian church.
The crown prince is expected to visit Ismailia today where he will tour some of Egypt’s national projects including the new channel of the Suez Canal.
In preparation, the Ismailia Governorate has decorated the route along which they will travel with flags.
Later they will attended a performance of the show “Salem Nafsak” (Surrender Yourself) at the Cairo Opera House.
The Coptic Orthodox Church announced that Prince Mohammed would visit the main St. Mark’s Coptic Cathedral in Cairo.
Pope Tawadros II met King Salman at his residence during his visit to Cairo in April 2016.
Also on Sunday, US President Donald Trump called El-Sisi to discuss with him “regional issues” and “ways of combating terrorism,” a statement from the Egyptian presidency said.
Prince Mohammed stressed that his keenness to conduct his first foreign visit as Crown Prince "reflects the depth and strength of relations between Egypt and Saudi Arabia, which are bound by common history and one destiny".