The family of the victim, now 20, sued the Boy Scouts, alleging the organization was negligent in its handling of the matter.
A judge ruled earlier this month that the plaintiffs could use the Scouts' secret "perversion files," which outline years of molestation claims and incidents, as evidence in the trial, a ruling that opened the door to possible public release of the files.
"We regret there have been times when the BSA's best efforts to protect children were insufficient, and for that we extend our deepest apologies to victims and their families," officials with the Boy Scouts said in a statement Thursday.
The lawsuit stemmed from a 2007 incident involving volunteer Scout leader Al Steven Stein, then 29, who was charged with abusing the 13-year-old Scout and two other boys.
Stein pleaded no contest to a felony child-endangerment charge. He was placed on five years' probation but violated it by having photos of nude children stored on his cellphone. He was sentenced to two years in prison but was paroled early and is now registered as a sex offender in Salinas.
Scout officials said they could not disclose terms of the settlement. The victim's attorney could not be reached for comment.
"While we can't comment on the specifics related to this matter, even a single instance of child victimization or abuse is intolerable and unacceptable," the organization said in a statement.
In regard to the perversion files, also known as the Ineligible Volunteer Files, Scout officials said "the behavior in these reports runs counter to everything for which the BSA stands."
"Nothing is more important than the safety of our youth members," they said. "The Ineligible Volunteer Files exist solely to keep out individuals whose actions are inconsistent with the standards of Scouting, and Scouts are safer because those files exist."
They also said the Scouts' national council reviewed all the files from 1965 to the present and reported to law enforcement any incidents that had not already been reported.