CAS said in a statement the appeal was against a decision taken during the FIFA Congress in May to not vote on a proposal by the PFA in which it sought the "recognition of its rights to run football activities in accordance with the FIFA statutes".
FIFA instead chose to vote on an alternative proposal in which the FIFA Council was granted a time limit until the end of March 2018 to study and evaluate reports from the FIFA Monitoring Committee Israel-Palestine.
The dispute centres on six teams from lower divisions of the Israeli league who are based in settlements in the West Bank and play their matches there.
The PFA says this is contrary to FIFA statutes which state that a member country's teams cannot play matches on the territory of another association without permission.
The PFA has also complained that Israel hampers its activities, including limiting the movement of players between the West Bank and Gaza, and that it has barred some international travel.
Israel has cited security concerns for its actions and the Israeli FA, which is a member of European soccer body UEFA, says it is not responsible for the actions of its government.
The FIFA committee convened for the first time more than a year and a half ago after being set up following a heated exchange at the FIFA Congress in May 2015, when the PFA was persuaded to drop its proposal for a ban of Israel.
In its appeal to the CAS, the PFA requests that the decision by FIFA not to vote on its proposal be declared null and void, that the decision that was passed in its place be revoked and that FIFA be ordered to immediately vote on the PFA’s proposal.CAS said a decision on the appeal would be issued at a later date following the exchange of written submissions and the completion of a hearing.