The visit, announced on Twitter by the royal palace in Doha and Mr El Sisi's office, was described by the Qatari news agency as the start of a “new era” in relations between the two countries.
It is Mr El Sisi's first visit to Qatar since he took office in 2014, a year after the military removed Mohammed Morsi from power after mass protests against his divisive, one-year rule.
"The visit crowns the intensive bilateral talks held recently and which are aimed at bolstering bilateral relations on all levels," an Egyptian presidential statement said.
"The president and his brother, the emir of the State of Qatar, will discuss bilateral relations and consult each other on regional and international questions that interest both of them and which require the unification of efforts to protect national Arab security."
Qatari Emir Sheikh Tamim visited Egypt in June when his energy-rich nation’s investments in the North African country were high on the agenda of talks with Mr El Sisi. Co-operation in the energy and agriculture sectors was also discussed.
In March, Cairo said Qatar planned to invest $5 billion in Egypt. Meanwhile, QatarEnergy announced an agreement with US company ExxonMobil to acquire a 40 per cent stake in a gas exploration block off Egypt’s Mediterranean coast.
Cairo had joined Saudi Arabia, the UAE and Bahrain in severing diplomatic ties with Doha in June 2017. This was over Qatar's support for the Muslim Brotherhood and soft line on Iran.
The dispute was resolved and relations were restored in January last year.
The Egyptian leader's visit comes at a time when the most populous Arab nation is in the grip of an economic crisis. This has been caused, in large part, by the damaging fallout from the Russia-Ukraine war and the coronavirus pandemic before it.
During his visit, Mr El Sisi will meet representatives of Qatari companies and members of the Egyptian-Qatari business council, Reuters reported.
In June, Egypt's finance ministry said Qatar had made $3bn of deposits in Egypt's central bank three months earlier. It added that an additional $2-3bn of investments were under discussion.
That was on top of deposits of $5bn from Saudi Arabia and $3bn from the UAE to Egypt's central bank in February-March this year, the ministry said.
Both the UAE and Saudi Arabia have also made recent investments in Egypt through their sovereign wealth funds.