The vote was delayed after an allegation of electoral fraud in the first round earlier this month.
Former military coup leader Julius Maada Bio received the most votes in the first round.
He now faces ruling party candidate Samura Kamara who is an economist by training.
Mr Maada Bio received 43.3% of the vote in the first round.
But in Sierra Leone the president is elected by absolute majority and if no-one gets 55% then it goes to a run-off.
President Ernest Bai Koroma is stepping down as president after serving two five-year terms. He chose Mr Kamara as his successor to run as president for the All People's Congress (APC).
Mr Maada Bio, who is leading the main opposition Sierra Leone People's Party (SLPP), lost to Mr Koroma in the last election. But Mr Maada Bio had already ruled the country briefly.
The 53-year-old was part of a group of soldiers who overthrew the government in 1992. Four years later he staged another coup and ruled Sierra Leone between January and March 1996.
Media captionWhat are the challenges for the next president of Sierra Leone?
Whoever wins this time, one of the greatest challenges for the new leader will be to improve healthcare following the devastating Ebola outbreak in 2014.
It killed nearly 4,000 people yet there are still only 200 doctors serving the country of seven million people.
The run-off was originally due to take place on Tuesday but the High Court ordered a delay after a member of the ruling party alleged there had been electoral fraud in the first round.
But the court rejected a petition by the ruling APC seeking an indefinite suspension of the run-off to allow for a forensic audit of the 7 March vote.
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