El-Sissi, who last summer ousted Egypt's first freely elected president, is likely to win the two-day vote by a landslide.
But he is looking for a strong turnout to show international critics that his removal of Islamist Mohammed Morsi reflected the will of the people.
The election is a powerful contrast to 2012 presidential elections, which were the first after the toppling of longtime autocrat Hosni Mubarak by a popular uprising the year before.
This time, the Brotherhood is out of the race, crushed under a ferocious crackdown that has killed hundreds of Morsi's supporters and arrested thousands more since his removal.
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El-Sissi has been elevated by a surge of nationalism fed by media lauding him as the nation's Savior. His only opponent in the race is leftist politician Hamdeen Sabahi, who finished third in the 2012 election.
"He is a military strict man. He will grip the country and bring security to the street," said Olfat Sayed Hasanein, a university professor who voted for el-Sissi. "We cannot afford any more failures."
El-Sissi, wearing a suit and tie, cast his vote at a school in the upscale Cairo district of Heliopolis, as women cheered and ululated to greet him. "The whole world is watching to see how the Egyptians will make history," he told reporters.