A statement from the president's office said that another five prisoners were also pardoned. It wasn't immediately clear when they will walk free.
The activist's lawyer, Khaled Ali, said that Abd el-Fattah is expected to be released from Wadi Natron Prison, just north of Cairo, immediately after the state's decision is published in the country's official gazette, which he expects is likely within the next two days.
Laila Soueif, Abdel-Fattah's mother, said that she was heading to the prison where her son is held.
"I won't rest until he is out," she said.
Abd el-Fattah was a leading voice in the country's 2011 Arab Spring uprising and has gone on multiple hunger strikes while behind bars.
His ordeal became emblematic of the fraying of Egypt's democracy.
The activist took part in the 2011 uprising that toppled autocratic former President Hosni Mubarak, and later was active in protests against human rights abuses as well as military trials of civilians.
He was first sent to prison in 2014 for participating in an unauthorised protest and allegedly assaulting a police officer, before being released in early 2019.
He was arrested again in September 2019 during a security crackdown that followed rare anti-government protests in Egypt, and after more than two years in pre-trial detention, an emergency security court sentenced him to five years for spreading false news.
When his release date came up in September 2024, authorities refused to count his time in pre-trial detention and ordered him held until January 3, 2027.
"My heart will explode," his sister Mona Seif posted on Facebook, relieved about the news of his pardon.
The pardon by President Abdel-Fattah el-Sissi came after an independent rights group submitted a petition to the president's office earlier this month.
The petition had seven names. It wasn't immediately clear if the seventh person was pardoned or not.
The National Council for Human Rights, acted on behalf of the families of the prisoners.
It urged el-Sissi to consider Abd el-Fattah's situation and that of the six others on "health and humanitarian grounds," and earlier this month el-Sissi's office said he had ordered relevant authorities to look into it.
The NCHR said in a statement on Monday afternoon that it welcomes the presidential pardon decision, describing it as a "step that underscores a growing commitment to reinforcing the principles of swift justice and upholding fundamental rights and freedoms".
Abd el-Fattah's family waged a desperate campaign to pressure Britain — whose citizenship Abd el-Fattah had obtained that year through his UK-born mother — to help secure his freedom and take him in.
When Egypt failed to release Abd el-Fattah last September, his mother, Soueif, began her own hunger strike in Britain, but became seriously ill and ended the strike in July.
Australian journalist Peter Greste, who was once jailed for 400 days in Egypt, joined Abd el-Fattah's mother on a hunger strike for 21 days.
An influential blogger, Abd el-Fattah, hails from a family of political activists, lawyers and writers.
His late father was one of Egypt's most tireless rights lawyers, his sisters — British citizens as well — are also political activists, and his aunt is the award-winning novelist Ahdaf Soueif.
Abd el-Fattah's most dramatic hunger strike came in 2022, as Egypt hosted an annual UN climate summit in the Red Sea resort of Sharm el-Sheikh.
That strike ended when Abd el-Fattah lost consciousness and was revived with fluids.
Leaders of Britain, France and Germany said they sought Abd el-Fattah's release in private talks with el-Sissi during the climate conference.
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