The meeting, a day after a donor conference for Gaza, was part of whirlwind tour by the US diplomat to bolster a campaign against Islamic State group jihadists in Iraq and Syria.
Egypt is one of the top recipients of US military aid, but relations between the two countries were rocked by the 2013 military overthrow of the elected Islamist president Mohamed Morsi.
Washington reacted to the ensuing crackdown on Morsi supporters by suspending part of its military aid, but has since moved to mend relations with its influential Arab ally.
"Secretary Kerry made clear the US wants to do even more to assist Egypt to grow and prosper economically and to help address Egypt's energy issues," a State Department official said after the meeting.
"The Secretary also emphasised the importance of a vibrant civil society and giving all Egyptians space to make their voices heard," the official added.
Egypt has given civil society groups a November deadline to register with the government under a law that right groups say is restrictive.
Meanwhile, Sisi, a former army chief who led Morsi's ouster last year, has continued a crackdown on his Islamist opponents who hold scattered demonstrations that often result in clashes with police.
The crackdown has extended to secular dissidents and several journalists as well.
Kerry said that in past visits to Cairo that he had had "candid conversations with President Sisi about the challenges that both of our countries face".
He told reporters on Sunday that US-Egypt ties remained strong as the "government undertakes significant reforms and works towards economic transformation for all Egyptians".
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Egypt still had to "prove to the world that the country is stable and open to business" as it seeks to restore its economy after years of political upheaval since the ousting of former strongarm leader Hosni Mubarak in early 2011.
The top US diplomat revealed that US energy giant General Electric might be able to help Egypt improve its power grid.
Washington has found itself walking a delicate tightrope in its ties with Cairo, keen to ensure that democracy is nurtured while maintaining relations with a key regional and military ally.
After his talks with Sisi, Kerry flew to Paris where he will meet French Foreign Minister Laurent Fabius.
On Tuesday, he is due to have talks with Russian Foreign Minister Sergei Lavrov, seeking to resolve yet another conflict -- the fighting in eastern Ukraine.
Western countries are trying to shore up a September 5 ceasefire deal in Ukraine which has been routinely breached in the country's east by pro-Russian separatist groups.
The complex civil war in Syria, as well as US efforts to raise a coalition to fight the Islamic State group, will also dominate the two veteran diplomats' talks in the French capital.
"We very much expect that these talks will turn out to be constructive," Russian foreign ministry spokesman Alexander Lukashevich said last week.
Kerry will then travel to Vienna to meet officials from another US adversary, Iran, as he seeks to hammer out a deal on reining in Tehran's nuclear programme by a November 24 deadline.