President Pierre Nkurunziza, whose government has repeatedly been accused of rights abuses, will step down after 15 years. His ruling CNDD-FDD party candidate, retired army general Evariste Ndayishimiye, is running against opposition leader Agathon Rwasa and five others.
The election is meant to usher in the first democratic transition in 58 years of independence for the impoverished east African nation, after widespread international criticism of its last election in 2015, when Nkurunziza ran for a third term.
His opponents said the move violated a peace deal that ended the civil war and boycotted the poll. The election sparked violent protests that drove hundreds of thousands of Burundians into exile. U.N. reports documented hundreds of killings and the torture and gang-rape of opposition activists. Donors withdrew funding in protest.
The government denies accusations of rights violations.
Rwasa, like Nkurunziza a former rebel leader, warned about possible electoral fraud in his final rally on Sunday.
"We know there is plan of election fraud, some are even intimidating people asking for their voter cards to vote for them," he said. "All of that is worthless."
The U.N. and the African Union said they "remain concerned about reports of intimidation and violent clashes between supporters of opposing sides", in a joint statement on Sunday.
There will be few election monitors after the government said they would have to go into a 14-day quarantine to prevent the spread of the new coronavirus.
The government expelled the national head of the World Health Organization (WHO) last week following public criticism that all parties were holding rallies despite the disease.
So far, the tiny East African nation has reported only 42 coronavirus case and one death. Testing remains very low, however - the nation of 11 million has carried out only 633 tests, according to the Africa Centres for Disease Control and Prevention.