At a press conference in Cairo on Monday, the NEA said 24,254,152 citizens voted in the elections at home and overseas out of more than 59 million eligible voters, representing a turnout of 41.5 percent, according to Al Ahram.
The NEA said the number of invalid ballots was 1,762,231 votes, amounting to 7.27 percent of the total votes. Mostafa Mousa, el-Sisi's only challenger, received just under 3% of the votes.
Sisi's serious contenders either withdrew, were sidelined or were detained.
"These are momentous moments for this nation. which will be written in letters of light under the title: battle for the love of Egypt", Lasheen Ibrahim, the election commission chief, said as he declared the vote free and fair.
It will replace the National Council to combat terrorism and extremism suggested by President Abdel Fatah El-Sisi in 2017.
However, Sisi's supporters say he has kept Egypt from slipping into further instability during his first four years in power.
The US State Department had earlier noted "reports of constraints on freedoms of expression and association in the run-up to the election".
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In 2014, el-Sissi won the presidency with 97 percent voter support, with turnout at more than 47 percent.
"The entire world heard your chants for the love of Egypt", he said.
The Trump administration on Monday congratulated President Abdelfattah al-Sisi of Egypt following his re-election.
People who boycotted the election and cannot show a good reason for missing the vote could face a fine of up to 500 Egyptian pounds (22 euros), the electoral commission has warned.
Russian Federation congratulated Mr Sisi on his election win ahead of the official results, and regional ally King Salman of Saudi Arabia called Mr Sisi on Monday to express support, saying his victory came as a result of strong efforts to combat terrorism.
Egypt has been suffering from a wave of terror attacks that have killed hundreds of policemen, soldiers and civilians since the army toppled former Islamist President Mohamed Morsi in July 2013.
Mahmoud Hilmi al-Sharif, deputy chairman of the Egypt's National Elections Authority and its spokesman, said that they have not received any appeals on the results of the public committees during the official period of the appeal, and that last Saturday and Sunday were dedicated for that goal.