"Religious freedom is a fundamental human right, and it is my fervent hope and prayer that respect for the inalienable rights and dignity of every man and woman will come to be increasingly affirmed and defended, not only throughout the Middle East, but in every part of the world," he said.
The trip, his first to the Middle East as pontiff, will include a visit to Israel and the occupied West Bank.
The papal pilgrimage is the "most awaited and perhaps most challenging trip so far" of Benedict's papacy, the Vatican said.
It said the fact that the trip was happening was "a sign of hope" that the pope could contribute to reconciliation in the Middle East.
Al Jazeera's Barbara Serra, reporting from Amman, said that the most challenging part of the pope's trip would be in Israel and the West Bank.
"The Vatican is keen to stress this is not a political trip ... but I think they would be naive to not think that every word the pope utters over the next few days is going to be viewed by someone through a political lense," she said.
"This is actually an incredibly sensitive time for any papal, especially as it comes just months after Israel's war on Gaza."
Benedict visited Amman's Regina Pacis centre for the handicapped on Friday before a meeting with the Jordanian royal family.
He was also expected to tour several Biblical sites, including Mount Nebo, where Moses is said to have seen the Promised Land from a distance, and celebrate mass in Amman, where 30,000 people are expected to attend.
Yousef Al-Sharif, Jordan's information minister, welcomed the pope's visit, saying: "We are really delighted that he will start pilgrimage from Jordan."
"What we want is a change in his policies, so that it is in harmony with the teachings of Jesus about love, peace, justice, equality and condemnations of crimes and Zionist terrorism"
Zaki Bani Rsheid,
Islamic Action Front
But Jordan's Muslim Brotherhood has criticised the pope's visit following a controversial papal speech in 2006.
The pontiff angered many Muslims when he quoted a medieval text that characterised some of the teachings of the Prophet Muhammad as "evil and inhuman".
The pope later said he was "deeply sorry" for the reaction his speech caused, and explained that the text did not reflect his own opinions.
The Brotherhood has called for an apology to the world's Muslims, saying the pope's statement of regret was "insufficient".
Jordan's opposition Islamic Action Front party has also called on the pope to apologise for the speech, which they said targeted Islam.
"What we want is a change in his policies, so that it is in harmony with the teachings of Jesus about love, peace, justice, equality and condemnations of crimes and Zionist terrorism," Zaki Bani Rsheid, the head of the party, told the AFP news agency.
The pope has said he is visiting the Middle East as "a pilgrim of peace" in a region plagued by violence, injustice, mistrust and fear.
But he angered many Jews in January when he lifted the excommunication of Richard Williamson, an ultra-conservative British bishop, who denied the use of gas chambers in the Holocaust.
Benedict admitted the Vatican made mistakes regarding the move, but he called on Catholics to stop infighting over the affair.
"That this overlapping of two opposing processes took place and momentarily upset peace between Christians and Jews, as well as peace within the church, is something which I can only deeply deplore,'' he wrote in a letter to the world's Roman Catholic bishops in March.