Kerry, the highest-ranking US official to visit since President Abdel Fattah al-Sisi came to power, was to press the former army chief during his lightning trip to instal greater political freedoms and discuss security challenges.
Since Islamist president Mohamed Morsi was toppled by Sisi in July 2013, a government crackdown on his supporters has left more than 1,400 people dead in street clashes and at least 15,000 jailed.
Kerry's visit comes a day after an Egyptian court confirmed death sentences for 183 Islamists, including Muslim Brotherhood chief Mohamed Badie, after a speedy mass trial that sparked an international outcry.
"The Secretary will discuss a variety of issues covering our bilateral relationship as well as regional issues, including Iraq, Syria, Libya, Israeli-Palestinian relations and the extremist and terror threats we all face," said State Department spokesperson Jen Psaki.
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Kerry's latest diplomatic mission, that will also see him visit Amman, Brussels and Paris, is expected to focus on uniting Iraq's fractious leaders and repelling insurgents whose lightning offensive has displaced hundreds of thousands, alarmed the world and put Prime Minister Nuri al-Maliki under growing pressure.
US officials announced in April they planned to resume some of the annual USD 1.5 billion in mostly military aid to Cairo, including 10 Apache helicopter gunships for counterterrorism efforts in the Sinai Peninsula.
But the aircraft remain in storage in the US, an official confirmed today.
Sisi won some 97 per cent of the vote in May elections nearly a year after the toppling of Morsi, and installed an interim government.