The body of the child beauty queen was found bludgeoned and strangled in her family's home on Dec. 26, 1996.
The grand jury accused both John and Patsy Ramsey of helping someone who committed murder, but prosecutors at the time declined to pursue the charges due to lack of evidence.
The documents did not identify who the alleged killer was, but the grand jury alleged that the Ramseys intended to delay or prevent the arrest of the alleged killer.
The Ramseys maintained their innocence, and in 2008, former District Attorney Mary Lacy cleared them based on new DNA testing that suggested the killer was a stranger, not a family member.
Patsy Ramsey died of ovarian cancer in 2006, the year a school teacher was arrested in Thailand after falsely claiming to have killed JonBenet. John Ramsey fought the unsealing of the documents, saying they are incomplete and further inflame false allegations.
Boulder Police Chief Mark Beckner said the case remains open, but it's not an active investigation.
The Associated Press contributed to this report.