She had been sexually assaulted and beaten to death with a rock, authorities said.
The case was cold until 2011, when DNA from the scene was matched with Seamons' DNA, which was in a national database.
In the courtroom Thursday, Seamons cried after the mother of 11-year-old Rebecca Lemberger said she forgave him for her daughter's death.
"I understand you were 15 years old. I don't understand why, but I forgive you," Nola Mahon said.
Seamons cried in response.
"I've thought about it for a long time, and these tears are too late. Nothing I can do can fix this," he said. "I don't expect the family's forgiveness."
He also told the court he wanted to clear his late father's name.
In 2012, Seamons sent a letter to The Salt Lake Tribune that said he suspected his father killed the girl.
The judge too became emotional at the sentencing, The Standard-Examiner reported.
"This case has been on the minds of the community for 30 years and has been a part of my entire career," DeCaria said. "I cannot understand how you can look this man in the eye and say you forgive him, but I appreciate that."
Seamons's guilty pleas were part of a deal with prosecutors, who agreed to reduce a murder charge to manslaughter.
Prosecutor Chris Shaw said the deal was fair because Seamons was a minor at the time of the crime.
DeCaria sentenced Seamons to serve terms of 1 to 15 years and 5 years to life at the same time for the two charges.
The terms will also run concurrently with a prison term Seamons has been serving in Idaho for a 2007 kidnapping conviction.
After his term in Idaho is complete in 2017, Seamons will be transferred to Utah's prison system.