The presidential and legislative election was originally set to take place on January 31, but was postponed due to irregularities.
Nearly 2 million people are registered to vote, according to the National Elections Authority.
Citizens displaced by violence will vote from nearby countries.
The presidential runoff comes after no candidate won majority in the first round in December. In addition to picking President, citizens will also vote in legislative elections after the Constitutional Court annulled the first legislative vote because of irregularities.
U.N. Secretary-General Ban Ki-moon urged all sides to maintain peace to ensure credible elections, warning that any perpetrators of violence will be held accountable.
Former prime ministers face off
Voters will choose between two former prime ministers: Anicet-Georges Dologuele and Faustin Archange Touadera.
Dologuele is promising to reform the country's troubled finances and attract foreign investment.
His rival, Touadera, is a former academic who is pledging to end corruption and bring unity.
Interim President Catherine Samba-Panza can't run because members of the transitional government are prohibited from participating in the election by the constitution.
Winner faces tough job
Whoever wins the presidency has a tough road ahead amid tensions between Muslims and Christians.
The nation plunged into chaos in 2013 when Muslim Seleka rebels overturned the government of former President Francois Bozize, prompting reprisals from Christian militias. Hundreds of thousands have been displaced by the violence and hundreds have been killed.
Peacekeepers accused of rape
Nearly 12,000 international peacekeepers are maintaining order in the country -- but not without controversy. Reports of rapes by peacekeepers have emerged.
Over the past 13 months, there have been more than 40 allegations of sexual abuse perpetrated by U.N. employees, according to U.N. data. Ban called the abuses "a cancer in our system" after firing the mission's peacekeeping chief.
The instability ravaging the country for nearly three years has left dire statistics.
It pointed out that over the past year, the number of hungry people in the nation has doubled.
Nearly 1 million people are displaced inside the nation or are seeking refuge in neighboring countries, according to the U.N.
And 41% of children under age 5 are chronically malnourished, UNICEF said.
Children have been dragged into the war, with as many as 10,000 recruited by armed groups during the crisis.
"Children will not vote this Sunday, their voices will not be reflected in the ballots, but the most serious political mistake would be to ignore those who will determine if the future holds a lasting peace," said Mohamed Malick Fall, the nation's UNICEF representative.