It is the first time a German civil court has allowed a case to be heard after the world's top sports court, the Court of Arbitration for Sport (CAS), has ruled against it, setting a precedent for potential similar cases.
"They (ISU) took everything from me but I keep on fighting," Pechstein told reporters.
"I now have the chance in a proper court, a German court. There I am confident because the ISU must now prove that I doped. There will never be a positive test from me and that is why I am confident."
The 42-year-old Pechstein, who is Germany's most decorated winter Olympian with five gold medals and nine in total, was banned by the ISU for two years in 2009 over irregular blood results, although she never failed a drugs test.
The ISU said the results were evidence she had been doping, a claim Pechstein refuted, saying it was a condition she had inherited from her father.
She continued to protest her innocence and took her case to the CAS which upheld the suspension, before then turning to German courts and demanding more than four million euros ($4.67 million) in damages over lost revenues due to the suspension.
The Munich court said in a statement its ruling "did not recognise the decision by CAS" adding that the ISU decision on the ban was "void".
The decision by the Munich Appeal Court will now require the confirmation from the Federal Court of Justice with the ISU having said it would take the matter to Germany's top court for civil jurisdiction before the case can be heard in a courtroom again.
Pechstein remains active as a skater and narrowly missed out on winning a medal at the 2014 Winter Olympics in Sochi.
(Reporting by Karolos Grohmann; Editing by John O'Brien)
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