The move suggests ISIS is planning further attacks against Christians in the North African country.
The Vatican said in a statement Thursday that the duo would meet up May 24.
The most populous communist state coming together with the largest Christian church would unite 2.6 billion people—a potentially seismic alliance.
Pope Francis hopes to improve Christian-Muslim ties following a wave of attacks on the country's Coptic minority.
"Power is like drinking gin on an empty stomach," the pope said.
Pope Francis is expected to address the International Peace Conference in Cairo at the end of April.
ISIS claimed responsibility for a rocket fired from the Sinai on Monday.
A Vatican official said Egypt has promised to do all it can to protect the leader of the Catholic world.
Pope calls the Syrian chemical weapons attack an "unacceptable massacre."
The pontiff is visiting an area in northern Italy that was hit with earthquakes in 2012.
The pope's recent suggestion that the Catholic Church discuss celibacy vows harks back to an earlier version of church practice.
Pope Francis met with Rwandan President Paul Kagame at the Vatican on Monday.
"Work gives us dignity," Pope Francis said.
Roman Catholic church head says bible reading will help people resist daily temptations.
Pope Francis was the victim of a poster campaign by critics who see him as tacking too far to the left.
The posters, which surfaced overnight, were quickly covered up by city authorities.
'Being afraid or rejoicing beforehand because of something that might happen is, in my view, quite unwise,' pope says.
The move will be a gesture of goodwill to a controversial figure, according to a Duterte aide.
In his year-end message, the pontiff says 'we have condemned our young people to have no place in society.'