Rafsanjani and a controversial aide of incumbent Mahmoud Ahmadinejad had been ruled unsuitable, the interior ministry said yesterday.
The Guardians Council, a conservative-dominated vetting body, omitted Rafsanjani, who served as president from 1989 to 1997, from its list of eight approved candidates.
It also excluded Esfandiar Rahim Mashaie, a confidant of Ahmadinejad and his former chief of staff.
The approved list of candidates for the June 14 election is dominated by conservatives close to supreme leader Ayatollah Ali Khamenei, the ultimate decision-maker in the Islamic republic.
More From This Section
A heavyweight until eight years ago when Ahmadinejad beat him in the 2005 presidential election, Rafsanjani has lost much of his political stock in recent years.
In particular, he drew the ire of the ruling establishment in 2009 when he openly questioned the handling of the controversial election that had given Ahmadinejad a second term.
That vote provoked massive street protests and claims of fraud, which were crushed in a heavy-handed crackdown.
Rafsanjani, who will turn 79 in August, currently chairs the Expediency Council, Iran's highest political arbitration body.
Mashaie, the other main candidate disqualified, had been personally endorsed by Ahmadinejad.
The United States accused the clerical leadership of seeking to tighten its grip on power.
"It appears that Iran's unelected Guardian Council, which is unaccountable to the Iranian people, has disqualified hundreds of potential candidates based on vague criteria," State Department spokesman Patrick Ventrell said.
"The Council narrowed the list of almost 700 potential candidates down to eight officials based solely on who the regime believes will represent its interests, rather than those of the Iranian people," he told AFP in an email.