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Uhuru Kenyatta, who is seeking a second term, won in August but the poll is being held again over irregularities.
Opposition candidate Raila Odinga has called on his supporters to join him in boycotting the ballot.
A bid to delay the election fell apart after only two out of seven Supreme Court judges showed up for a hearing.
One judge, Deputy Chief Justice Philomena Mwilu, failed to appear after her bodyguard was shot and wounded by unknown gunmen on Tuesday.
The Supreme Court annulled the original election in August by a 4-2 majority, saying there had been “irregularities and illegalities”.
Some international observers have reduced their involvement in the poll because they say the conditions are not conducive for a free and fair election.
‘Resistance movement’
Election commission chief Wafula Chebukati said the polls would open at 06:00 (03:00 GMT) after being given assurances by the authorities.
“Based on assurances given to this commission by the relevant authorities and security agencies… the elections as scheduled will go on tomorrow, 26 October 2017,” said Mr Chebukati.
But he also complained of threats to the electoral commission’s staff and said he said he could not guarantee their security while at work.
Speaking live on a private Kenyan TV channel, Mr Odinga called for “free, fair and credible elections”.
“From today we are transforming the Nasa [National Super Alliance] coalition into a resistance movement.”
Earlier, Chief Justice David Maraga announced that a petition to delay the vote could not be heard because only two of the court’s seven judges had shown up.
In addition to Ms Mwilu, one judge was said to be ill and receiving treatment abroad, another was out of the capital Nairobi and could not get a flight back, and two others were unavailable for undisclosed reasons.
The main opposition party says this is no coincidence and is a sign of the intimidation of the country’s independent institutions, the BBC’s Tomi Oladipo reports from Nairobi.
Anyang Nyong’o, governor of the western Kisumu county, an opposition stronghold, said people would be justified to rebel if the vote went ahead on Thursday.
“If the government subverts the sovereign will of the people… then people are entitled to rebel against this government,” Reuters news agency quoted him as saying.
Opposition protesters have blocked roads and lit bonfires in the city of Kisumu itself.
The government had declared Wednesday a national holiday to allow people to travel to places where they were registered.
Political tensions have sparked fears of unrest. After the 2007 poll, violence left over 1,600 people dead and thousands displaced.
By: BBC
