Floyd Durr, already serving a 125-year prison sentence for sexually assaulting other girls, was sentenced to life in prison plus 30 years for the murder and sexual assault of Ryan Harris.
Ryan was beaten and sexually molested in July 1998, then dumped in a weedy lot on Chicago's South Side, where she was found dead the next day.
Authorities initially said two boys, then 7 and 8, confessed to the crime. It took almost a month before testing on the girl's clothing showed the boys couldn't have been responsible.
DNA tests later led prosecutors to Durr.
The plea deal Monday was opposed by Ryan's mother, who wanted Durr to face the death penalty. Last week, Sabrina Harris sought to have a special prosecutor appointed in the case, but Judge Stanley Sacks rejected the request.
Sacks said that while he sympathized with Sabrina Harris, she had no right as a private citizen to seek the death penalty against a defendant.
Families for the two boys initially accused in the case settled lawsuits against the city of Chicago for more than $8 million. One alderman called the case "one of the most shameful episodes in our city's history."
Attorneys for the two boys claimed that police framed the children and ignored evidence of their innocence, but police have long denied that. The city did not admit any wrongdoing in its settlements with the families.