The countries signed agreements to "activate" a 60 billion Saudi riyal ($16 billion) investment fund they agreed to set up in 2016, and another deal on environmental protection, at a short televised ceremony attended by the two leaders.
In February, 14 global and Egyptian rights groups published a joint statement, accusing Sisi of having "trampled all over even the minimum requirements for free and fair elections".
Prince Mohammed and Sisi emphasized coordinating efforts to bolster joint Arab cooperation.
Salman has encouraged strong economic cooperation with Egypt and Sisi's ambitious projects.
A Saudi government source said Prince Mohammed's choice of Egypt for his maiden overseas trip as crown prince "reaffirms Saudi-Egyptian cooperation at the highest level".
In 2015, during a visit by King Salman to Cairo, the two countries agreed on the transfer of two Red Sea islands to Saudi Arabia, sparking protests in Egypt.More news: Diabetes 'is FIVE different diseases' not two, doctors discover
Prince Mohammed's visit comes ahead of Egypt's presidential polls later this month, with Sisi expected to win a second four-year term.
The two officials discussed bilateral ties and ways to develop them in various fields.
Mr Hariri posted a selfie with Prince Mohammed and the kingdom's ambassador to the United States after their meeting in Riyadh late on Friday at the end of a three-day visit.
Rady also highlighted the significance of the visit's timing in light of the "great challenges now taking place in the Middle East, which require mutual coordination between Egypt and Saudi Arabia".
The two men discussed the developments in the region and bilateral relations between their two countries.
In response to the Egyptians who opposed the deal, the Egyptian leadership repeatedly said the two islands were originally Saudi but leased to Egypt in the 1950s.