Kerry met his counterpart Sameh Shoukry to patch up troubled relations between the two countries with a pledge of support.
He later met President Abdel Fattah al-Sisi, and was also scheduled to fly to Qatar to meet Gulf Arab counterparts.
Egypt and other regional states such as Saudi Arabia are suspicious of Iran, which they see as bent on destabilising them.
"There can be absolutely no question that if the Vienna plan is fully implemented, it will make Egypt and all the countries of this region safer than they otherwise would be or were," Kerry told a joint news conference with Shoukry.
"If Iran is destabilising, it is far, far better to have an Iran that doesn't have a nuclear weapon than one that does."
Ties between the US and Egypt had frayed after then army chief Sisi overthrew Islamist president Mohamed Morsi in 2013.
