Jalili, 47, filed his papers at the interior ministry but did not speak to reporters, an AFP correspondent said.
A veteran of the 1980s war with Iraq in which he lost his right leg, Jalili had previously not expressed an intention to seek office.
He heads Iran’s team in negotiations with world powers over Tehran’s controversial atomic activities, which the West fears are aimed at developing a military capacity — a claim denied by the Islamic republic.
Ahmadinejad is constitutionally barred from seeking a third consecutive term.
His successor is expected to face an array of challenges, including Iran’s worsening economy targeted by international sanctions over its uranium enrichment activities.
Earlier on Saturday, veteran diplomat Ali Akbar Velayati and Tehran mayor Mohammad Baqer Qalibaf also registered to stand in the election, the first since 2009 which saw massive street protests erupting after Ahmadinejad’s re-election.
Before taking over as the secretary of Iran’s Supreme National Security Council, Jalili was a deputy foreign minister, as well as holding a position in the office of Iran’s supreme leader Ayatollah Ali Khamenei.
All decisions on key state affairs rest with Khamenei, including on the nuclear issue.
In Istanbul on May 15 Jalili is scheduled to meet the European Union’s top diplomat Catherine Ashton, who represents the so-called P5+1 group of Britain, China, France, Russia and the United States plus Germany in nuclear talks with Iran.
Their last meeting in April in the Kazakh city of Almaty left the two sides “far apart”, according to Ashton.
Iran is expected to wrap up the five-day registration of candidates on Saturday, leaving the fate of the hopefuls in the hands of the Guardians Council, an unelected body controlled by religious conservatives appointed by Khamenei.
The council will vet the candidates to ensure they adhere to constitutional conditions of being faithful to the principles of the Islamic republic and its official religion, before announcing the final list of hopefuls no later than May 23.
Approved candidates will then have three weeks to campaign before polling day on June 14.
