A police official said officers fired tear gas and made arrests at one of the protests in the Cairo neighbourhood of Mohandessin.
The deal to hand over two islands in the Straits of Tiran, signed during a visit by Saudi King Salman to Cairo last week, has provoked a storm of criticism against Egyptian President Abdel Fattah al-Sisi.
Egyptian police had warned Egyptians yesterday not to hold demonstrations after activists called for rallies across Cairo after the Friday Muslim prayers, held at noon.
Demonstrations not approved by the police have been banned.
The calls for the protests were made by secular and Islamist activists who accuse Sisi of "selling" the islands in return for Saudi investments.
The Egyptian government says the islands were Saudi to begin with, and were leased to Egypt in 1950.