Some 250 travelling from each diocese throughout the country will take part in a reception for the pontiff when he arrives in Cairo on Friday.
Organiser of the pilgrimage, Fr Hani Kiroulos from the Coptic Catholic Church said: "Many young people have the desire to participate in the huge event."
The pope's visit is due to take place just three weeks after two suicide bombings at Coptic churches in Alexandria and Tanta on Palm Sunday left at least 45 people dead.
The young Catholics are making the pilgrimage with the support of Aid to the Church in Need which is helping cover the costs of meals and accommodation.
Neville Kyrke-Smith, national director of ACN (UK), said: "We are pleased to support Egyptian Christians welcoming Pope Francis to their capital this April.
"We pray for our Catholic family - the 3,000 children and our Holy Father's safety as well as all other Christians gathering with their Muslim neighbours as an expression of tolerance after recent attacks by extremists."
"Our prayers go out to them as they embark on their peaceful pilgrimage. We wish them all a safe and spiritual enriching journey."
The trip will last five days with the schedule including a visit to the Virgin Mary shrine, and voluntary work at shelters for the vulnerable and at hospitals.
ACN's executive president, Johannes Heereman, spoke of the charity's material help and prayers for the trip's success: "Together with our financial support we will launch a social media prayer action to accompany this important visit of the Holy Father."