In the elections on March 31, the opposition Republican People's Party (CHP) narrowly defeated Erdogan's AK Party in Turkey's largest city in a rare election defeat to the president amid growing economic problems.
But after weeks of appeals by the Justice and Development Party (AKP), Turkey 's Supreme Electoral Council in May overturned elections for what he called "irregularities". The opposition described the decision as a "coup" against democracy, raising the risks for the second round.
The loss of the city for a second time, according to Reuters, would be "embarrassing" for Erdogan and could weaken what until recently appeared to be his iron fist to power. Erdogan himself served as mayor of Istanbul in the 1990s.
The Turkish economy is suffering from a recession and the United States, Turkey's NATO ally, has threatened to impose sanctions if Erdogan is to buy a Russian missile defense system.
A second loss to the Justice and Development Party (AKP) could shed more light on what the Republican People's Party (CHP) candidate for mayor Akram Emamoglu described as a waste of billions of lira in Istanbul's budget of about $ 4 billion.
Voting starts in Istanbul at 8 am local time (05:00 GMT) and ends at 5 pm. The results will be announced in the evening.