Another threat will come from Esfandiar Rahim Mashaei, the eminence grise behind outgoing President Mahmoud Ahmadinejad, both of whom are die-hard political foes of Khamenei, who is the ultimate power in Iran.
But all the 680 Iranians who've registered candidacies with the Interior Ministry last week must be vetted by the 12-member Council of Guardians, which is firmly controlled by Khamenei.
Rafsanjani and Mashaei announced their candidacies Saturday shortly before registration for the June 14 poll closed.
Political insiders are betting Mashaei, widely viewed as a Rasputin-like figure who controls the rabble-rousing Ahmadinejad, won't be approved as a candidate for the Guardians Council.
Ahmadinejad, first elected in 2005, cannot run for a third term but he wants Mashaei to succeed him in what many see as a power grab similar to Russian President Vladimir Putin's tag-team deal with Prime Minister Dmitry Medvedev.
The constitutional watchdog -- made up of six clerics and six jurists -- has 10 days to decide on the final list of candidates, half a dozen a most.
While the disqualification of Mashaei, whose promotion to vice president by Ahmadinejad was blocked by Khamenei two years ago, is seen as a slam dunk, Rafsanjani's candidacy is likely to be approved.
But once campaigning starts, Rafsanjani, 79, a founder of the Islamic Republic and two-term president in 1989-97, is likely to be heavily targeted by Khamenei's propaganda machine.
Rafsanjani's participation in the election is necessary to give the illusion of democracy in action running against rivals who are close to Khamenei, such as Saeed Jalili, Iran's leading nuclear negotiator; Tehran Mayor Mohammad-Baqer Qalibaf; and former foreign minister Ali Akbar Velayati.
However, Rafsanjani has secured the backing of Iran's reformist bloc, and its popular leader, Mohammad Khatami, who was president in 1997-2005.
The reformists have taken a severe drubbing by the clerical regime and its strong arm security services over the last few years but amid widening economic hardship caused by Western sanctions over Tehran's contentious nuclear program, many Iranians are expected to vote against the regime.
Rafsanjani, who was once Khamenei's ally and played a key role in getting him elevated to supreme leader to succeed Ayatollah Ruhollah Khomeini in 1987, also has considerable support among the Bazaaris, the merchant class.
There's a lot riding on this election, both in terms of domestic policy and Iran's relationships with the West and regional powers like Saudi Arabia and Turkey.
It's no secret in Tehran that Khamenei opposes Rafsanjani's participation in an election held amid the power struggle between the supreme leader and the populist Ahmadinejad who since winning a second term in 2009 in a violently disputed poll has battled to secure greater powers for the presidency at the leadership's expense.
So there are fears the June election could be as disruptive as the 2009 protests, the worst internal unrest since the Islamic Republic was born in 1979.
It's ironic that Ahmadinejad won re-election only because Khamenei backed his protege and then found himself being stabbed in the back.
"Khamenei has two choices now: To let Rafsanjani win the election and get public credit that only he can resolve the country's problems or to go for a massive crackdown, the end of which would not be clear," a senior reformist politician observed.
There are signs of voter apathy based on the belief Khamenei will decide who wins anyway. So the regime needs a hefty voter turnout to give the election legitimacy.
"To have a peaceful election with a credibly high turnout ... the regime's power centers, notably the Revolutionary Guards, had planned to engineer an election where several fundamentalist candidates loyal to Ayatollah Khamenei could compete with each other," the Financial Times observed.
"Rafsanjani's entry into the race has emerged as a game-changer however."
Velayati has hinted that Rafsanjani wouldn't be allowed to triumph.
"We would not step back under any conditions from our determination not to let anyone who has differences with the supreme leader to take hold of the country's affairs," he said.