Peggy Knobloch went missing in Bavaria in 2001 and her remains were found last July, in a thickly wooded part of Thueringen.
DNA was found on a tiny piece of cloth at the scene, and matched that of Uwe Boehnhardt. He was in a neo-Nazi cell accused of murdering 10 people.
A woman linked to him is on trial.
Beate Zschaepe is accused of involvement in those killings. She denies that and also denies membership of the National Socialist Underground (NSU) cell.
The group carried out a series of racially motivated murders, bomb attacks and robberies between 2000 and 2007.
The discovery that the cell had acted for so long with impunity shocked Germany. An investigation found that police had underestimated the threat from violent neo-Nazis.
Nine of the 10 victims of the group's murder spree were of Greek or Turkish origin.
The revelation about Boehnhardt's DNA in connection with the Peggy Knobloch case throws up new questions. Police are checking to see whether there was accidental contamination of evidence, because her body and that of Boehnhardt were examined at the same lab.
Another theory is that Boehnhardt's DNA could have got there if he had given a blanket, a vehicle or something else to the girl's killer.
He was found dead in a caravan with Uwe Mundlos, allegedly a fellow gang-member. They apparently committed suicide together in 2011 in the eastern city of Eisenach, shortly before Ms Zschaepe handed herself in.
Peggy Knobloch disappeared when walking home from primary school on 5 May 2001.
Her remains were found some 150km (95 miles) from Eisenach.
Investigators are still hunting for Peggy's killer. They say several paedophiles lived near her or met in a hotel near her home in north Bavaria, Der Spiegel news reports (in German).
DNA traces from a notorious neo-Nazi who died in 2011 have been found in woods where the body of a nine-year-old girl was hidden in eastern Germany.