FIFPro said the dispute had highlighted its concerns about the Lausanne-based Court of Arbitration (CAS), sport's highest tribunal, which was previously criticised by the soccer union in March.
"FIFPro expresses its moral, political and financial support for...Claudia Pechstein, who is leading a legal battle...to defend her innocence and her right to a fair and impartial legal procedure since 2009," the union said in a statement on Tuesday.
FIFPro added that "Pechstein's fight for her own rights can positively impact those of thousands of professional athletes around the world, among them the 65.000 footballers represented by FIFPro."
The five-times Olympic champion was banned by the International Skating Union (ISU) for two years in 2009 over irregular blood results, although she never failed a drugs test.
CAS rejected her appeal against the ban, as did the Swiss Federal Tribunal (SFT).
But a Munich court said in January it would allow Pechstein to go ahead with a lawsuit demanding more than four million euros ($4.37 million) in damages over lost earnings.
"Every athlete as a citizen and worker has the right to a fair process and to be judged in an independent and impartial court," said FIFPro.
"The decisions of the regional courts in Germany in Claudia Pechstein's case have confirmed that this right was not duly granted by CAS at the time of her anti-doping case."
FIFPro said CAS had played a fundamental role in shaping the football transfer system "which continues to operate with detrimental effect on the players' rights."
FIFPro complained that the appointment of arbitrators on CAS panels failed to provide athletes with equal representation or ensure independence.
CAS were not immediately available for comment.
FIFPro first expressed its criticism in March when it said CAS lacked independence, equal representation and accessibility.
"Urgent reform is needed in which athletes must play an active and equal role," added FIFPro.
"We are convinced that Ms. Pechstein with our support will take a historic step in the near future to help install an arbitration system, which respects the rights of all athletes."
(Editing by Amlan Chakraborty)
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