Turnout was the main challenge facing el-Sissi, as the opposition had called on Egyptians to boycott the election, calling it a "farce" after potentially serious opponents dropped out of the race or were barred from running.
Other, more heavyweight would-be challengers were all sidelined, detained or pulled out.
The almost three percent of the vote not won by the incumbent president went to the unknown politician Moussa Mustafa Moussa, an ardent supporter of el-Sissi's who entered the race at the last minute and did not campaign.
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Turnout was 41 percent, despite efforts to get as many Egyptians as possible to polling stations during last week's vote.
Human rights groups have frequently slammed al-Sisi for his crackdown on protesters and the Egyptian news media.
He said 92.73% of the votes were valid from the roughly 24 million cast, while nearly two million ballots were spoiled.
In a press conference on Monday, the National Election Authority announced the victory of Sisi over Ghad Party Chairman Moussa Moustafa Moussa in the 2018 presidential election.
Egypt's President-elect Abdel Fattah al-Sisi.
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"We have noted reports of constraints on freedoms of expression and association in the run-up to the elections".
In 2013, el-Sissi led the overthrow of the country's first democratically elected but divisive president, Mohamed Morsi.
"The election was an epic of love dedicated to Egypt", said head of the election commission, Lasheen Ibrahim.
There were no presidential debates and Sissi himself did not appear at any official campaign events, although he spoke at a number of ceremonies. Since then, authorities have waged a sweeping crackdown on dissent, jailing thousands of Islamists and several prominent secular activists.
In February Sisi ordered the armed forces launched their most comprehensive campaign yet to end the five-year-old militant insurgency.
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