Disability Rights Mississippi filed suit in 2009 in U.S. District Court to challenge conditions at the 30-bed Lauderdale County Juvenile Center in Meridian.
Among the lawsuit's allegations were that youngsters were locked in crowded cells all day and denied care for mental health and medical issues.
The agreement calls for those practices to end and establishes a community advisory board.
A notice of the settlement was filed with the court April 30.
Plaintiffs' attorney, Sheila Bedi, said the settlement shows the county's commitment to protect detained youths.
Lee Thaggard, an attorney who works for the county, didn't immediately return a call Tuesday.