An Egyptian judge quashed President Abdel Fattah Al Sisi’s agreement to cede two Red Sea islands to Saudi Arabia, a deal that sparked some of the country’s largest protests in years over what was viewed as the sale of sovereign Egyptian territory.

Mr. Sisi agreed to give Saudi Arabia control of the two disputed islands, Tiran and Sanafir, in April during a visit by Saudi King Salman to Egypt. The islands lie in the Straits of Tiran, a narrow passage between Egypt’s Sinai province and the Saudi coast that links the Red Sea with the Gulf of Aqaba.

Tiran and Sanafir historically belonged to Saudi Arabia but have been controlled by Egypt since 1950, when Riyadh transferred custody of the islands to Cairo to better protect Arab interests against Israel.

Khaled Ali, a former presidential candidate and lawyer leading one of several lawsuits to block the agreement, said the court had ruled that the islands remain within the territory of Egypt and fall under Egyptian sovereignty.

“Any change in their situation in any way in favor of any country is prohibited,” he said, citing the ruling on Tuesday.

The court’s decision isn’t final and could be appealed by Mr. Sisi’s government and overturned by a superior court. However it has also yet to receive parliamentary approval in Egypt.

Saudi Arabia’s Ministry of Foreign Affairs didn’t immediately respond to a request for comment in response to the court’s verdict. The Saudi Shura Council, an unelected advisory body to the king, has already approved the agreement.

A decision to contest the verdict would represent a challenge to one of Mr. Sisi’s biggest Egyptian supporters, the judiciary, which is constitutionally protected from executive interference but has routinely ruled in favor of the president, handing down harsh life sentences and death penalties against his opponents.

At the same time a decision to abide by the ruling could upset Saudi Arabia, Mr. Sisi’s biggest ally in the region in the face of rising tensions with Iran.

The Saudis have thrown financial support behind Egypt through the signing of deals worth as much as $22 billion, mostly to finance Egypt’s energy needs and infrastructure improvements. The agreement to cede Tiran and Sanafir would clear the way for construction of a 9.3-mile bridge across the Straits of Tiran, linking the two countries.

When the deal was signed with King Salman in April, the Egyptian president said that he hadn’t surrendered Egyptian territory but had instead restored Saudi Arabia’s rightful ownership, citing government records that proved Riyadh’s legal claim over the islands.

“We didn’t relinquish even a grain of sand,” Mr. Sisi said, saying the transfer of control of islands came after years of study and negotiation that began before he assumed the presidency.

However the government’s declaration of the islands’ transfer sparked one of the largest public protests in Egypt in years, with hundreds of demonstrators and activists arrested.

Lawyers and prominent politicians accused the president of selling the islands to Saudi Arabia, a reference to the billions of dollars in trade and loan agreements Riyadh has signed with Egypt since Mr. Sisi came to power in 2014.