But the plan caused street protests a year ago from many Egyptians who say their sovereignty over the islands dates back to a treaty from before Saudi Arabia was founded.
The court ruled in January that the islands were always Egyptian, but the Court of Urgent Affairs overturned the ruling in April, saying that the lower court had no jurisdiction over the agreement.
Previous administrative court rulings invalidated the deal while a later verdict from the court of urgent matters halted the invalidation ruling.
Egypt's high administrative court has defended an earlier decision to annul the transfer of two Red Sea islands to Saudi Arabia, local media and judicial sources said.
Wednesday's decision only applies to the two courts involved, not to parliament, which has approved the deal. But in June past year the country's highest administrative court ruled Egypt's sovereignty must stand.
"The ruling (on Tuesday) signifies that the land is Egyptian", said Khaled Ali, a lawyer who argued at the administrative court that the islands belonged to Egypt.
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The verdict would affirm that any attempt to transfer the islands would be considered unconstitutional "even if the president ratified the agreement", Ali said.
"Now the ball is in the president's court", Ali said.
Critics say the islands belong to Egypt and that their transfer is linked to the billions of dollars the Saudis have given to support Egyptian President Abdel Fattah el-Sisi's government. The latter had previously ruled in favor of the bilateral deal enabling the transfer in 2016.
Opponents of the deal say the government is willing to hand over the islands in exchange for funds from the oil-rich kingdom.
Lying at the mouth of the Gulf of Aqaba, the islands can be used to control access to the Israeli port of Eilat.
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