Archbishop Justin Welby started the meeting on Sunday at the Presidential Palace in Heliopolis by offering condolences for the deaths of the 20 Coptic Christian Egyptians who were killed in Libya.
Archbishop Justin's visit to Egypt comes amid the release of another by video IS showing around 30 Ethiopian Christians being massacred.
The film released on social media sites shows 15 men being beheaded on a beach and another group of the same size, in an area of shrub land, being shot in the head. Both groups of men are referred to in a subtitle as "worshippers of the cross belonging to the hostile Ethiopian church".
The archbishop also met with religious and political leaders on his visit, including the Coptic Christian Pope and the Grand Imam.
Archbishop Justin presented the notes from the families of British terror victims in person to Bishop Tawadros, the Pope of Egypt's Coptic Christians.
Mr Welby's spokesman told Sky News he carried the messages after a grieving relative of British aid worker David Haines, who was murdered by IS last year: "came to see him a few weeks ago and asked him to take these letters with him".
"He personally took 21 letters with him and has handed them over," the spokesman added.
"The essence of the visit is to show solidarity following the murder of the Coptic Christians.
"It is also reminding people of what has happened.
"The people he has met so far have been genuinely delighted that he has made this very brief visit here to pledge his support and stand by them."
Justin Welby has called for more support for Christians facing persecution. He also met the key authority on Sunni Islam, the Grand Imam of Al Azar, during his stay in Cairo.
