Rafsanjani, who will be 79 in August, filed his papers at the interior ministry during the final minutes of the five-day registration process which wrapped up today.
"I came to serve. It is the right of the people to choose me or not," Iranian media quoted him as saying.
Rafsanjani has been isolated since the 2009 presidential election, which saw massive street protests against the disputed re-election of President Mahmoud Ahmadinejad.
He then called for the release of people rounded up during the demonstrations.