The 75-year-old Ayatollah Ali Khamenei, who has final say on all state matters in Iran and has been the country's top leader since 1989, was reported to be recovering.
The official IRNA news agency said the operation, which was described as "routine," was successful. There were no immediate details on what had prompted the surgery or the underlying medical condition.
Iranian state TV said that Khamenei told the station just ahead of the surgery that there was "no room for concern" and that it was a routine operation. The TV aired a brief footage of Khamenei just ahead of the surgery in which he asked people to pray for him.
Khamenei served as Iran's president for eight years before becoming the supreme leader in 1989. He has proved a powerful defender of the rule by clerics created by his predecessor.
He thwarted the movement in support of a reformist presidential candidate, Mir Hossein Mousavi, in 2009, and when hundreds of thousands of Iranians rose up around the country marching in the streets, some overtly denouncing him, he stepped forward to crush the protests.
At the same time, Iran has sought to extend its influence in the Middle East through its ally Syria and Islamic militant groups despite attempt by US-backed Arab governments to contain Iran.
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