Several activists protested in different parts of the country including in Cairo, Alexandria, el-Sharqeya, Mansora and other areas and accused Sisi of selling the islands in return for Saudi investments.
Over the past week, President Sisi has come in for severe criticism over his decision which had triggered angry reactions from many Egyptians, who consider the move as an insult to their national pride.
The two islands were under Egypt's control for over 60 years.
Street protests without prior permission from police are banned in Egypt after a controversial law was passed in this regard in 2013.
In one of the major protests, thousands of people rallied outside the Press Syndicate in downtown Cairo even as the security forces cordoned the area preventing other protests from marching to Tahrir Square.
The protesters held placards and chanted slogans like 'Our land is our honour' and 'they've sold the land to Saudis' to express their anger over the decision.
They also used slogans similar to the 2011 revolution including, "people want the regime to fall", "bread, freedom and social justice" and "Leave".
Egyptian government said the two islands at the mouth of the Gulf of Aqaba belong to Saudi Arabia, which asked Egypt in 1950 to protect them from Israel.
Israel captured the islands in the 1967 Middle East war, but handed them back to Egypt under the provisions of the 1979 peace treaty.
A recent statement by Egypt's government said that agreement of demarcation the maritime borders between Egypt and Saudi Arabia is an important achievement that will make the two countries benefit economically.
Last Wednesday, President Sisi had defended his decision saying that it was made in line with the "documents with the Egyptian state institutions such as the Ministry of Foreign Affairs, the Ministry of Defence and the General Intelligence Service and it stuck to the 1990 presidential decree which was submitted to the United Nations.
