The Egyptian billionaire, who in addition to Harrods also owned the Premier League football club Fulham, was accused last year in a BBC documentary of several cases of rape and assault. BBC had then spoken with over 20 women who worked at the exclusive department store from the 1980s onwards.
"Even though nothing can compensate for the assaults that the victims have been subjected to, Harrods wants all those who are entitled to receive this compensation", it states in a statement on Harrods' website.
Those applying for compensation do not need to have been employed at Harrods, but must have a "sufficiently close connection" to the department store or to al-Fayed's role there to be approved.
All those who apply will also receive an apology from Harrods.
The police say they have been contacted by more than 90 people who accuse al-Fayed of assault.