The afternoon meeting comes six months after Sisi's rise to power. According to religious news agency I.Media he will be accompanied by Egyptian Foreign Minister Sameh Choukri and three other ministers.
Sisi will then meet Italian Prime Minister Matteo Renzi in Rome at 1800 GMT, Renzi's office said.
Sisi, who led the coup last year that ousted elected Islamist president Mohamed Morsi, hopes to strengthen Egypt's ties with the Holy See, according to diplomatic sources cited by religious news agency I.Media.
Signup to our newsletter and follow us on Facebook and Twitter!
The talks are likely to address the relationship between the Roman Catholic Church and Sunni Islam's main theological centre, the famed Al-Azhar University which fell out with the Vatican in 2011.
Al-Azhar broke off relations after Francis's predecessor Benedict XVI said not enough was being done to prevent the persecution of Christians in remarks perceived by some to be offensive to Islam.
Christians, mostly Orthodox Copts, make up some 10 percent of Egypt's 86 million population.
Sectarian violence during Morsi's government saw some of the community emigrate after a series of attacks on churches.