The case filed at the Court of Arbitration for Sport (CAS) is aimed at voiding a FIFA resolution, passed at its Congress last month, to push back a decision on the Israeli clubs until March 2018 at the latest.
The PFA argues that the presence of six Israeli clubs on its territory is in breach of FIFA statutes, which forbids another member association playing on another territory without permission.
The Palestinians had called for a resolution stating that as a full FIFA member the PFA has the right to block Israeli teams from playing on its land.
In its CAS appeal, the PFA called for FIFA's postponement decision to be declared "null and void" and that "FIFA be ordered to immediately vote" on the issue, the Lausanne-based court said in a statement.
Israel argues that FIFA rules are unenforceable as there is no permanent border. Israel accuses the PFA of trying to use a football flap to establish borders.
The disputed clubs controversy has now been presented to five separate FIFA Congresses.
FIFA president Gianni Infantino has said the body's final decision will likely come before the March 2018 deadline, indicating it will be resettled at the next Congress in India in October.