Dank, who ran the supplements programme at Australian Rules club Essendon in 2012, was found guilty of 10 breaches of the AFL's anti-doping code in April but cleared of 21 others. Dank denies any wrongdoing.
"WADA has appealed the AFL Anti-Doping Appeals Tribunal decision to clear Mr Stephen Dank... of 21 charges of the league's drug code," WADA director-general David Howman said in a statement.
"After a thorough examination of the evidence contained within the case file, WADA has decided to lodge its independent right of appeal to the Court of Arbitration for Sport (CAS)."
The AFL anti-doping tribunal also found 34 former and current players of the Essendon Bombers club not guilty of taking banned supplement Thymosin beta-4 in March.
WADA said last month those verdicts would also be appealed at CAS, the court of last resort for disputes in the sporting world.
Australian Sports Anti-Doping Authority (ASADA) chief executive Ben McDevitt supported WADA's stance.
"ASADA notes and welcomes the decision by WADA to appeal the AFL Anti-Doping Tribunal's decision to clear Mr Dank of 21 doping charges," he said in a statement.
"ASADA will fully support the WADA-initiated appeal to the Court of Arbitration for Sport."
ASADA and the AFL launched a joint investigation into Essendon's supplements regime more than two years before the verdicts were handed down.
The saga overshadowed Australia's richest football code for two seasons, with allegations of impropriety being made from all sides.
An independent review in 2013 commissioned by Essendon castigated the club's management for governance failures that produced a "disturbing picture of a pharmacologically experimental environment" during their 2012 season.
Essendon, one of the AFL's oldest and most successful teams, were subsequently barred from the competition's 2013 playoffs, slapped with a record fine and had their head coach James Hird banned for 12 months for bringing the league into disrepute.
(Reporting by Nick Mulvenney; Editing by John O'Brien)
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