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Harvard does not charge a financial aid application fee. However, the financial aid application does include submission of the CSS Profile, an application independent of Harvard but that will normally require the payment of a fee. 

For CSS Profile fee waiver requests: If you are a US Citizen or Permanent Resident you will automatically be evaluated for a waiver of the CSS Profile application fee at the point that you submit your CSS Profile data to the College Board. The College Board is wholly responsible for these fee waivers and will grant a waiver using their guidelines.  You can learn more on their website here: https://cssprofile.collegeboard.org/fee-waivers.

International students for whom the cost of the CSS Profile is prohibitive or who live in countries from which the College Board cannot process payments can follow these instructions to apply through our alternate application process.

Admission application fee waiver requests are explained here: (https://college.harvard.edu/resources/faq/paying-admissions-application-fee-hardship-my-family-can-i-get-waiver)