British-Egyptian dual national Mr El-Fattah, who has been in prison for six years, was a leading voice in the country’s 2011 Arab Spring uprising.
He went on hunger strikes behind bars and his ordeal became emblematic of Egypt’s democratic backsliding.
State media reported that the president also pardoned another five prisoners. It was not clear when they will walk free.
Mr Abd El-Fattah’s mother, Laila Soueif, went on hunger strike in the UK at the end of last year in a bid to win her son’s liberty.
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