Washington's top diplomat, who describes himself as an evangelical Christian, is on a tour aimed at reassuring regional US allies after Washington's shock decision to withdraw US troops from Syria.
On Thursday evening he visited the Cathedral of the Nativity of Christ and the Al-Fattah Al-Alim mosque in Egypt's New Administrative Capital, 45 kilometres (28 miles) east of the capital.
At the mosque, he praised Egypt's "freedoms here in this houses of worship, these big, beautiful, gorgeous buildings where the Lord is clearly at work".
"This is a special country where President Sisi clearly made a point by putting this, this largest cathedral in the Middle East here in this place," Pompeo said, calling the building "a great symbol of hope".
"Sisi is moving his country to a more inclusive future," Trump said.
Coptic Christians, who account for around 10 per cent of Egypt's population, have been hit by a string of sometimes deadly attacks by the Islamic State group in recent years.
They have long complained of official discrimination.
Asked about the role of governments towards religious minorities, Pompeo said they had "an obligation to make sure that every individual can choose to worship the way they want or choose".
"It's wonderful that here in Egypt it's possible," he said.
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