He will attend the funeral of Archbishop Anba Abraham, the head of the Coptic Church in the Holy Land who died yesterday at the age of 73.
Egyptian Copts were forbidden from visiting Israel by their late Pope Shenouda III in protest at Israel's occupation of east Jerusalem.
Shenouda passed away in 2012 after leading the ancient orthodox church for 40 years.
"The visit is to attend the funeral and nothing more," church spokesman Boulos Halim told AFP.
Despite the ban, hundreds of Egyptian Copts have visited Israel over the past few years during Easter.