The meeting took place late in the evening after Sisi arrived here on a three-day visit.
They met and discussed bilateral as well as regional issues, sources said.
Kerry, whose official engagement ended here yesterday and was scheduled to return to Washington, is likely to leave for Hangzhou in China for the G-20 summit beginning Sunday.
Earlier in the day, Sisi met External Affairs Minister Sushma Swaraj who called on him here.
Sisi told Swaraj that he wants to take anti-terror cooperation between the two countries to a "whole new level" and pitched for "strong collective action" against radicalisation.
He will hold wide-ranging talks with Prime Minister Narendra Modi tomorrow and both sides are set to sign a number of MoUs thereafter.
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