"The parliamentary elections scheduled for next year are of great importance," said Grand Ayatollah Ali Sistani, 90, in an online statement after the bilateral meeting.
Iraqis should be encouraged to participate "widely," he added, while warning that failing to hold the polls on time or in a free and fair way would "threaten the unity and future of Iraq's people."
Sistani does not make public appearances and typically issues a weekly Friday sermon through a representative.
He avoids meeting political figures, but has traditionally made an exception for the UN, which is seen as unbiased.
This year, the cleric has been quieter than usual - weekly prayers stopped in late February with the onset of the coronavirus pandemic, which also sparked fears for Sistani's health.
On Sunday, Sistani hosted the UN's top representative in Iraq Jeanine Hennis-Plasschaert in his modest home in the shrine city of Najaf, 10 months since their last meeting.
"If done in the right way, in the right and credible way, they could open an important chapter for the country," she said, referring to early elections.
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Prime Minister Mustafa al-Kadhemi had announced in late July that Iraq would hold parliamentary elections nearly a year early, seeking to make good on one of the main promises he made when he came to power earlier this year.
Sistani has himself been a proponent of early elections since last year, when unprecedented anti-government protests rocked Baghdad and the Shiite-majority cities of the south.
The cleric had been increasingly sharp in his criticism of the current fragmented parliament, which was elected in May 2018.
The 329-member body has voted in favour of electoral reform ahead of next year's elections but has yet to decide on key elements, including district size.
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