Victory would hand Sisi a six-year term in which immediate priorities would be taming near-record inflation, managing a chronic foreign currency shortage and preventing spillover from the conflict between Israel and Gaza's Hamas rulers.
Voting is spread over three days from Sunday, with results due to be announced on December 18.
As voting began on Sunday morning, small crowds gathered at polling stations in Cairo, where pictures of Sisi have proliferated in the weeks leading up to the election. Riot police were deployed at entrances to Tahrir Square in the centre of the capital.
Critics see the election as a sham after a decade-long crackdown on dissent. The government's media body has called it a step towards political pluralism.
Three candidates qualified to stand against Sisi in the election, none of them high-profile figures. The most prominent potential challenger halted his run in October, saying officials and thugs had targeted his supporters - accusations dismissed by the national election authority.
Authorities and commentators on tightly controlled local media have been urging Egyptians to turn out to vote, though some people said they were unaware when the election was taking place in the days before the poll. Others said voting would make little difference.
As army chief, Sisi led the 2013 ousting of Egypt's first democratically elected president, Mohamed Mursi of the Muslim Brotherhood, before being elected to the presidency the following year with 97 per cent of the vote.
Since then he has overseen a crackdown that has swept up liberal and leftist activists as well as Islamists. Rights groups say tens of thousands have been jailed.
Sisi and his backers say the crackdown was needed to stabilise Egypt and counter Islamist extremism. He has presented himself as a bulwark of stability as conflict has erupted on Egypt's borders in Libya, and earlier this year in Sudan and Gaza.
Sisi was re-elected in 2018, again with 97 per cent of the vote.
The election campaign has been low-key, with Sisi following a typical program of opening an arms trade fair, inspecting roads and sitting in on examinations for candidates to join military and police academies in the week leading up to the vote.
