Larijani, who is embroiled in a public political feud with President Mahmoud Ahmadinejad, was speaking at a religious site in Qom, the city he represents in parliament, on the occasion of the 34th anniversary of the 1979 Islamic revolution.
Shortly after starting his speech, a group of people began chanting slogans against him, according to the Iranian Labor News Agency (ILNA).
It said Larijani spoke for two to three minutes more, but then a crowd of about 100 Ahmadinejad supporters began throwing shoes and matchbox-sized clay tablets, used in prayer by some Shi'ites, towards him.
Throwing shoes is a serious insult in Muslim countries.
Larijani tried to quiet the crowd, saying "We shouldn't compromise this great celebration with such actions," according to the Mehr news agency, which did not identify the assailants.
His feud with Ahmadinejad burst into the open last week when the president used a speech in parliament to accuse Larijani's family of corruption - a charge the family denies.
Infighting between Iran's top officials has intensified as June's presidential elections approach, and is happening despite calls by Supreme Leader Ayatollah Ali Khamenei for elected officials to stop their bickering ahead of the vote.
ILNA said some people at the ceremony tried to defend Larijani from the objects, but the crowd began moving in the direction of the speaker and he was forced to leave.
Parliamentary news agency Icana said "a few" people had tried to "create chaos" by chanting slogans against Larijani.
(Reporting By Yeganeh Torbati, Editing by William Maclean and Richard Meares)