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Protect Academic Freedom Act - Amends the Higher Education Act of 1965 (HEA) to prohibit institutions of higher education (IHEs) from being eligible to receive any form of financial assistance under such Act if the Secretary of Education determines that they are participating in a boycott of Israeli academic institutions or scholars.

Directs the Secretary, no later than May 1 of each year, to: (1) identify and make publicly available a list of all IHEs participating in such boycott, and (2) notify each IHE that is so identified of its designation as a participant in such boycott.

Gives IHEs 30 days after their identification as a boycott participant to request the Secretary to waive their ineligibility for financial assistance under the HEA.

Makes the funding prohibition inapplicable to funds available for student financial aid.