Since the overthrow of Hosni Mubarak in 2011 raised hopes of new freedoms, the country of 85 million, where one in four Egyptians lives in poverty, has been convulsed by political, security and economic turmoil.
The vote - with initial results expected hours after polls close at 9 p.m. (1800 GMT) on Tuesday evening - means Egypt will likely revert to rule by men from the military after Sisi toppled the country's first freely elected leader, Mohamed Mursi of the Muslim Brotherhood.
Former army chief Sisi faces only one challenger: the leftist politician Hamdeen Sabahi. Other candidates who contested the 2012 election won by Mursi did not run, saying the climate was not conducive to democracy.
Despite calls for a big turnout by Sisi and media loyal to the army, the turnout on Monday appeared lower than in previous elections. With Sisi seemingly assured of victory, he needs a good turnout to shore up his legitimacy.
Lines at 20 Cairo polling stations visited by Reuters consistently over the past three years appeared shorter than in previous elections. The interior minister said turnout was good.
As polls were about to close after the first day of voting on Monday, there was no sign of a late rush. The supervisor of a polling station in a working-class district of Cairo told Reuters fewer than 30 percent of registered voters had shown up.
Earlier on Monday, it was hard to find anyone who planned to vote for Sabahi in lines of voters where young Egyptians - the generation that drove the "Arab Spring" uprising - were conspicuous by their absence.
Many of Sisi's supporters said they voted for stability rather than Western-style democracy, which they felt had brought chaos and hardship into their lives.
"The Egyptian people and democracy, it doesn't work like it does in Europe," said Ahlam Ali Mohamed, a 47-year-old housewife in Alexandria, who voted for Sisi. "I voted today because I want to feel safe."
Although he enjoys the adulation of many Egyptians, Sisi, 59, faces serious challenges including an economy in crisis and a campaign of Islamist violence that has spiraled since he overthrew Mursi.
To the Islamists, he is the author of a coup followed by a bloody crackdown that killed hundreds of Mursi supporters and landed thousands more in jail. Secular dissidents who led the January 25 uprising against Mubarak have also been imprisoned.
Human Rights Watch estimates the number of political dissidents and Islamists in detention at more than 20,000.
At the same time, several hundred members of the security forces have been killed in a campaign of violence by radical Islamists since last July. The last year has been the bloodiest period of internal strife in Egypt's modern history.
The Brotherhood and its allies, which had declared it "the election of the presidency of blood", issued a statement saying their call for a boycott had been widely observed. The group has been declared a terrorist organization by the state, which accuses it of turning to violence - a charge it denies.
VOTER QUEUES SHORT
In the rural province of Fayoum, south of Cairo, and in the city of Alexandria, both places where Islamists have strong support, voter queues were short throughout Monday.
Many of those who opposed Sisi said the election lacked democratic credibility.
"These elections are a theatre play. I won't give them legitimacy with my vote," said Ahmed Hassan, a 37-year-old doctor. "We didn't come out in a revolution against Mubarak's regime to get it back after all those people died."
Sisi won 95 percent of votes cast in advance by Egyptians abroad, but an opinion poll by the Washington-based Pew Research Center suggests a more mixed picture, with Sisi viewed favorably by 54 percent and unfavorably by 45 percent.
As Sisi voted in Cairo on Monday, he waved to supporters, who shouted "President, President!"
"Today Egyptians are going to write their history," said Sisi.
It is the second time Egyptians are electing a president in two years. And it is the seventh vote or referendum since 2011.
Once president, Sisi will nonetheless have to meet the high expectations of those who backed him so enthusiastically in the hope that he can tackle poverty, unemployment and other social problems.
He will also be expected to address the corruption, cronyism and inequality between rich and poor that caused the 2011 revolution that overthrew Mubarak.
Sabahi's campaign team complained of violations including the arrest of one of its members.
Since the army overthrew the king in 1952, Egypt has been ruled by a succession of military men - Gamal Abdel Nasser, Anwar Sadat and Mubarak. That pattern was briefly interrupted by Mursi's divisive year in office, during which important institutions of state resisted his authority.
The 2012 election won by Mursi was a tightly contested race fought by around a dozen candidates.
Sisi, quietly spoken former head of military intelligence, has in turn mobilized religion against the Islamists, presenting himself as a God-fearing defender of Islam.