The vote is being seen as a significant step towards restoring peace, stability and democratic government.
It comes after the seizure of power by a mainly Muslim rebel group in 2013 led to prolonged bloodshed.
Both presidential candidates, former prime ministers Faustin Touadera and Anicet Dologuele, have pledged to restore security and boost the economy.
Mr Dologuele served under President Ange-Felix Patasse between 1999 and 2001, and Mr Touadera was prime minister under President Francois Bozize between 2008 and 2013.
There are hopes that the poll will help turn the page on years of sectarian conflict.
Communal reconciliation and reigniting the country’s sluggish economy have featured prominently as campaign themes.
The Central African Republic is one of the world’s most unstable countries and was thrown into political chaos three years ago when mostly Muslim Seleka fighters toppled President Bozize.
Christian militias responded to Seleka abuses, with attacks carried out against the Muslim minority community.
The north-east of the country is now mostly under the control of Muslim rebels while Christian militias hold sway the south-west.
Thousands died in the fighting and roughly a fifth of the population is thought to have been displaced.
Mr Dologuele has promised voters a break from the country’s recent violent past, with the campaign slogan “united we will win”.
Mr Touadera is portrayed by supporters as a peacemaker who can bridge the Christian-Muslim divide.
There was a turnout of nearly 80% for the first round of voting in December.
Observers saw that as being a rejection of violence by the electorate.