Rafsanjani, who was president between 1989 and 1997, registered at the interior ministry in the closing minutes of the five-day registration process for the presidential vote which wrapped up today.
The final line-up of candidates will not be known until later this month when the Guardians Council releases the approved list of names after the vetting process.
"I came to serve. It is the right of the people to choose me or not," Rafsanjani was quoted by Iranian media as telling reporters.
Rafsanjani, who will be 79 in August, had polarised Iran's complex political spectrum in recent weeks by announcing that he was considering standing again.
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He has been isolated by ultra-conservatives since Ahmadinejad's disputed re-election in 2009 sparked massive street protests, leading to a heavy-handed regime crackdown and the arrest of hundreds of journalists, activists and reformist supporters.
Also today, Saeed Jalili, Iran's top nuclear negotiator and close figure to all-powerful supreme leader Ayatollah Ali Khamenei, unexpectedly showed up at the ministry and registered his candidacy.
The decisions by Rafsanjani and Jalili overshadowed earlier registrations of a handful of conservative hopefuls, including veteran diplomat Ali Akbar Velayati, Tehran mayor Mohammad Baqer Qalibaf, former Revolutionary Guards commander Mohsen Rezaei, ex-foreign minister Manouchehr Mottaki and former health minister Kamran Bagheri Lankarani.
According to the interior ministry, some 686 candidates have registered, including 30 women. Approved candidates will have three weeks to campaign before polling day on June 14.