Imam Khamenei went to the polling station at Imam Khomeini mosque in Tehran in the early hours of Friday.
After casting his vote, Imam Khamenei underlined the importance of the presidential and city and village councils elections, and called for mass-participation of the people.
Iranian voters started casting their ballots at 8 am local time (3:30 GMT) on Friday to elect their president for the next four years.
People throughout the country will also cast their ballots to elect members of city and village councils concurrent with the presidential election today.
Campaigning for today's presidential election kicked off in Iran after the Guardian Council released the list of 6 qualified candidates on April 21, although 4 have remained in the race now. Campaigning ended at 8:00 local time on May 18.
There are now 4 candidates left in the race after two of them gave up their bid. They include incumbent President Hassan Rouhani, member of the Expediency Council Mostafa Aqa-Mirsalim, former deputy judiciary chief Seyed Ebrahim Rayeesi and former vice-president Seyed Mostafa Hashemi-Taba.
Tehran's mayor and a Principlist candidate Mohammad Baqer Qalibaf announced in a statement on Monday that he has withdrawn his presidential bid in favor of Rayeesi, another candidate of the same front who now has the highest chance among the Principlist nominees to win the election.
Also incumbent Vice-President Eshaq Jahangiri announced withdrawal in favor of President Rouhani on Tuesday afternoon.
The vetting body examined the qualifications of more than 1,600 candidates who had signed up to run in the election on May 19.
According to presidential election laws, all Iranian nationals above 18 years of age are eligible to vote.
Iranian voters will go to over 63,000 polling stations in and outside the country today to elect their next president.
Observers predict a high turnout similar to previous elections in the Islamic Republic in the post-revolution era.
The next president of the country will be elected if one of the four candidates manages to secure 50 percent plus one of the votes, otherwise, a runoff between the two top contenders will determine the next president.