Abdul Fattah al-Sisi gained over 93% of the vote with ballots from most polling stations counted, state media say.
Turnout is expected to be about 46% despite a massive push to get more people to polling stations. Many groups boycotted the vote.
Abdul Fattah al-Sisi deposed President Mohamed Morsi last July after mass protests.
He has overseen a bloody crackdown on Mohamed Morsi’s Muslim Brotherhood movement in which more than 1,400 people have been killed and 16,000 detained.
The Brotherhood said it would boycott the vote, as did many liberal and secular activist groups.
The Islamist movement rejected the vote on Thursday with Tariq al-Zumar, a senior member of the Brotherhood, calling the process a “theatrical play, which did not convince anybody”.
Hamdeen Sabahi, the only other candidate in the election, said earlier his team had recorded “violations” in the voting process.
However, he rejected calls from his supporters to withdraw from the elections, saying it was not in the interest of Egyptians.
Hamdeen Sabahi secured fewer than 760,000 of the 24.7 million votes counted, and lost out in many regions to a high number of spoiled ballots, the state-run al-Ahram newspaper reports.
Hundreds of Abdul Fattah al-Sisi supporters took to the streets of Cairo in the early hours of Thursday as results emerged, waving Egyptian flags, setting off fireworks and honking their car horns.
The military-backed authorities had extended voting to a third day in the hope of boosting turnout.
But reports suggested many polling stations were almost deserted on Wednesday.
Egypt’s new president will inherit a crippled economy, a low level insurgency, and a bitterly divided nation.
He had aimed to win 40 million of 54 million registered votes, to show that he had the support of the majority of Egypt. In the event, it appears about 25 million voted.
In comparison, turnout for the previous presidential election between Mohamed Morsi and former PM Ahmed Shafiq was around 52%.
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