Sisi and King Abdullah II jointly condemned the "collective punishment" of Palestinians in Gaza, while warning of regional spill over.
"If the war does not stop", it would threaten "to plunge the entire region into catastrophe", read a Jordanian statement.
In separate statements issued after their meeting, the two leaders "affirmed their unified position rejecting the policy of collective punishment in the siege, starvation or displacement" of Palestinians.
A statement released by Jordan's royal court prior to the meeting said Sisi and King Abdullah II were to "discuss means to stop the Israeli aggression on Gaza."
The statement by the Jordanian royal court was released in response to air and artillery strikes on Gaza that were carried out by Israel amid war with Hamas militias — hostilities that started on Oct 7 and to date has killed over 1,400 people, mainly civilians and foreign nationals.
The Hamas-controlled health ministry reports the Israeli strikes have killed 3,478 people in the besieged Palestinian enclave.
Sisi and King Abdullah II were due for talks with U.S. President Joe Biden and Palestinian President Mahmud Abbas in Jordan this week, but the Arab nation cancelled the meeting after a deadly strike on a Gaza hospital.
Despite the cancelled meeting, Sisi on Thursday spoke to the U.S. Central Command chief Michael Kurilla about "the situation in Gaza," said the office of the North African leader.
The meeting between Sisi and King Abdullah II will happen on the same day that United Nations Secretary-General Antonio Guterres is expected in Cairo.
Egypt and Jordan were the first Arab states to normalize relations with Israel, in 1979 and 1994 respectively, and have since been key mediators between Israeli and Palestinian officials.
More discussions on aid delivery to Gaza were held in Cairo on Thursday amid a meeting between Egypt's Foreign Minister Sameh Shoukry and the United Kingdom's Foreign Secretary James Cleverly.
Shoukry's ministry said the two leaders discussed "the priority of delivering humanitarian and emergency aid to the people of Gaza."