Mr. Bush and his wife, Laura, went to the embassy to express sympathy about Saturday's pre-dawn bombings that killed dozens of people.
"Laura and I have come to your embassy to express our heartfelt sympathies for those who have lost their lives," the president said after writing a personal message in a book inside the embassy.
Mr. Bush said his visit was meant to "reiterate my country's strong desire to stand shoulder-to-shoulder with the people of Egypt and bring justice to those who killed innocent people."
The attackers, he said, "have no heart. They have no conscience. They have no ideology that is hopeful."
Egypt's ambassador to the United States, Nabil Fahmy, said the president's visit sent a strong message against terrorism.
"We continue to work together, resolute, to deal with this scourge, and ultimately, hopefully to develop in the Middle East an Egypt that is prosperous, stable and secure for all," Fahmy said.