"Inshallah (God willing), the Iranian people will create a new political epic. I advise all people to vote and do so in the early hours of the morning," said the Leader after casting his ballot in Tehran early Friday.
The Leader also condemned the remarks made by US officials about the presidential poll.
"The Iranian people... will do what is in their interest," Ayatollah Khamenei said.
Ayatollah Khamenei added that both officials and the nation are grateful to Almighty God for granting them another chance to be part of a move which is to determine the destiny of the country.
Polls across Iran opened at 08:00 local time (03:30 GMT) on Friday and will close at 18:00 (13:30 GMT). If there is a massive turnout the Interior Ministry can extend voting until midnight.
The Friday election will decide a successor to outgoing President Mahmoud Ahmadinejad.
The six candidates in Iran’s presidential election are President of the Expediency Council’s Center for Strategic Research Hassan Rohani, Supreme National Security Council Secretary Saeed Jalili, Expediency Council Secretary Mohsen Rezaei, Tehran Mayor Mohammad Baqer Qalibaf, former Foreign Minister Ali Akbar Velayati, and former Telecommunications Minister Mohammad Gharazi.
Former Majlis Speaker Gholam Ali Haddad-Adel and former First Vice President Mohammad Reza Aref withdrew their candidacies earlier this week.
Concurrent with presidential poll, Iranians are casting their ballots in the fourth city and rural council elections on Friday.