The pontiff told the five survivors, an unknown number of whom had been abused by priests, that clergy and bishops would be held accountable when they abuse or fail to protect children.
Many abuse survivors are angry at how the Vatican has dealt with allegations.
The Roman Catholic Church in the US has been embroiled in child abuse scandals.
US dioceses have made huge compensation payouts to victims.
Pope Francis met the five victims, all now adults who had suffered abuse as children, on September 27 at a seminary in Pennsylvania, his spokesman said.
The group – three women and two men – had been abused by clergy, family members or teachers, Father Federico Lombardi said in a statement.
Each was accompanied by a family member, he added.
The Pope was “overwhelmed with shame that men entrusted with the tender care of children violated these little ones and caused grievous harm,” he told bishops following the meeting, on the final day of his visit to the US.
Pope Francis told the victims who were abused by a member of the clergy that he was “deeply sorry” for the times when the abuse was reported, but victims or their families “were not heard or believed,” the Vatican said in a statement.
“Please know that the Holy Father hears you and believes you,” Pope Francis told the survivors.
The Pope listened to the survivors’ stories, prayed with them, and expressed his “pain and shame” in the case of those harmed by clergy or church workers, Federico Lombardi said.
Pope Francis “renewed his commitment” to ensure that victims are treated with justice, the guilty are punished, and to effective prevention in the Church and in society, the statement said.
However, survivors’ advocacy groups expressed some skepticism at whether the Pope’s words would lead to any change.
In June the Pope approved the creation of a tribunal to hear cases of bishops accused of covering up child abuse by priests.
In 2014, the UN strongly criticized the Church for failing to stamp out abuse and for allowing cover-ups.
At the end of a nine-day tour of Cuba and the US, Pope Francis is due to hold an open-air Mass in Philadelphia later on Sunday.
Pope Francis also met inmates at a prison in the city earlier in the day.
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