With 15 little-known candidates running against him, 71-year-old Bashir faces no real competition in the vote, which has already been criticised by the international community.
Voters will also elect national and state lawmakers in the three-day poll, with Bashir's ruling National Congress Party expected to dominate.
The streets of the capital were quiet as the vote started, after the government declared polling day a public holiday.
Bashir arrived at the St Francis School to vote around 11:00 AM (1330 IST), smiling and waving as he entered the polling station with one of his two wives. Journalists outnumbered voters.
"I came here because the elections are the right to choose who governs me," said 25-year-old Abdallah Mohammed Ali.
Around 100 policemen joined the handful of ordinary voters, piling out of trucks and minibuses to cast their ballots.
At polling stations in Khartoum's twin city Omdurman, there were also few voters.
Many residents had expressed little interest in the election.
"Everyone knows the result," said Mutawakil Babikir, a 43-year-old shopkeeper.
The elections are the second contested ballots since Bashir seized power in 1989.
Bashir toppled a democratically elected government in an Islamist-backed coup and is Sudan's longest-serving leader since independence.
Under his rule Sudan's economy has faltered, suffering badly from South Sudan's 2011 secession, which saw it lose nearly three-quarters of its oil resources.
Conflict has plagued South Kordofan and Blue Nile states since 2011, and the Darfur region since 2003.
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