Supporters are brushing aside concerns about human rights and hailing him as the strong leader the country needs.
Three years after the historic uprising against Hosni Mubarak, the vote is set to restore a pattern of rule by men from the military after Sisi toppled Egypt's first freely elected leader, Mohamed Mursi of the Muslim Brotherhood.
Voters lined up to cast ballots at heavily guarded polling stations from 9.00 am. Sisi faces only one challenger in the two-day vote: the leftist politician Hamdeen Sabahi.
"We see Sisi as a real man. Egypt likes a strong man," said Saber Habib, clenching his fist to illustrate his point as he waited to vote in the city of Suez, east of Cairo.
"We want the country to move forward and for the people to have bread," said the 64-year-old contractor.
Widely regarded as Egypt's de facto leader since he toppled Mursi after mass protests, Sisi, 59, faces manifold 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 mastermind of a bloody coup that led to a crackdown that has killed hundreds of Mursi supporters and landed thousands more in jail. Secular dissidents who led the 2011 uprising against Mubarak have also been imprisoned.
The Brotherhood and its allies have called for a boycott.
As he voted in Cairo, Sisi waved to supporters, who shouted "President, President!"
"Today Egyptians are going to write their history," said Sisi, who is seeking a big turnout by voters to provide him with a strong mandate.
The election is the seventh vote or referendum since the 2011 uprising that raised hopes for greater political freedoms. But three years on, after a failed experiment with democracy, many Egyptians say stability comes first.
Sisi won 95 percent of votes cast in advance by Egyptians overseas, but an opinion poll by the Washington-based Pew Research Center suggests a more mixed picture inside Egypt, with Sisi viewed favorably by 54 percent and unfavorably by 45 percent.
At one polling station in Cairo, all bar one person in a line of around 50 men said they would vote for Sisi, who has been lionized by media run by the state and big businessmen overwhelmingly supportive of the army.
"I'm voting for Sabahi because of his program and because Egypt needs a civilian president to begin building a democratic society like other countries have," said Fathi Abdelhamid, 58, a manager at an engineering firm.
Interrupting him, the person next to him said: "But most people want someone with experience, and that person is Sisi. Look at his experience in military intelligence. He knows how to work with the state."
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 - a pattern briefly interrupted by Mursi's one year in office.
The 2012 election won by Mursi was contested by around a dozen candidates, in stark contrast to this vote.
The Brotherhood has described the election as a farce.
"What happened in Egypt was wrong and the best message against it is to boycott this vote," said Abdel Karim Mohamed, a 45-year old accountant, speaking in hushed tones as he parked his motor-bike near a polling station.
Critics fear Sisi will rule Egypt with an iron fist, and that he will protect the political and economic interests of the generals and businessmen who amassed fortunes before the 2011 uprising which toppled Mubarak but remain influential.
Human rights groups have raised serious concerns about accounts of torture in police custody, and a court's decision to sentence some 1,200 Brotherhood supporters and members to death earlier this year drew criticism from Western governments.
"Egypt's presidential elections will not wipe the country's human rights record clean after 10 months of gross violations," rights group Amnesty International said in a statement.
Sisi has listed security and the economy as his primary concerns and said Egypt is not ready for a Western-style democracy - comments with echoes of the Mubarak days.
The militant campaign has killed several hundred members of the security forces since last July. Three South Korean tourists were killed in a bomb attack at a Red Sea resort in February.
The election will have a bearing on relations with the United States, which has linked the future of its long-standing military ties with Cairo to the political transition.
Following Mursi's overthrow and the crackdown, the Obama administration suspended much of its 1.3 billion US dollars in annual military aid to Cairo. But last month it announced it would resume some of the military assistance, partly to help in the fight against militants.
Monitors from the European Union and US-funded Democracy International are observing the vote, and more than 400,000 members of the security forces have been deployed to secure polling stations across the country.
As voting began, one of Egypt's state-run TV stations reported a bomb had exploded outside a polling station. The Interior Ministry denied the report, saying the noise was a car back-firing.