"Africa is threatened by cross-border terrorism," Sisi said, calling on leaders gathered in the capital of Equatorial Guinea to "firmly face up to this plague to preserve the dignity of our people and economies."
"This common threat demands that we reinforce our cooperation," said Sisi, whose attendance at the summit marks his country's grand comeback to continental politics.
Egypt was suspended from the AU bloc after Sisi toppled Islamist president Mohamed Morsi while he was army chief last July.
It is taking place in a sprawling town called Sipopo boasting 52 luxury presidential villas which President Teodoro Obiang Nguema had specially built for a previous summit in 2011.
Equatorial Guinea, sub-Saharan Africa's third largest oil producer, is plagued by accusations of human rights abuses and a political elite hoarding its wealth.