The voter turnout in the 2014 presidential polls, which Sisi won by almost 97 percent of votes against leftist politician Hamdeen Sabahi, was about 47.5 percent of some 53.8 million registered voters.
El-Sissi's sole challenger Moussa Mostafa Moussa is a little-known politician whose last-minute bid has been seen as mostly symbolic in order to give the election the appearance of a genuine contest.
The final results are expected to be officially announced on Monday.
The turnout of 47 percent in that year's election was sharply higher than this year's 40 percent despite appeals from Prime Minister Sherif Ismail for voters to fulfil their patriotic duty.
After the polls closed on Wednesday evening, el-Sissi issued a statement saying he was proud of the Egyptian people's behavior during the election.
The Egyptian administration has endeavoured to underpin political legitimation of Al-Sisi without shadow of high abstention, in face of appeals of opposition sectors to boycott elections.
"The scenes of Egyptians at polling stations will remain my source of pride and honour and a compelling proof of the greatness of our nation, whose most precious sons have offered [their] blood so that we can move together towards the future", he added. The election commission pledged the vote would be free and fair.
Judges supervising the polling centers said that out of 7,800 registered voters, some 3,000 cast ballots, or around 38 percent.
Other women, who also declined to be named, said they had been promised bags of food containing rice and vegetable oil in exchange for votes.
At the office of a logistics company in Cairo's working class Ward estate, employees collected national ID cards and informed people where they could vote.
Some people needed no inducement to vote.
Ashraf Ahmed, a 50-year-old ceramic sculptor, said while smoking shisha in a cafe: "I have only one wish and if accomplished, I will be very happy".
"Why didn't they have more than one candidate?" she asked, after casting her vote.
Some of his serious rivals withdrew citing restrictions, some were sidelined, others arrested.
The vote counting started right after closure of polling centres nationwide at 10 p.m. on Wednesday.
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