A court official said the man had confessed to his alleged crimes and was on trial.
He was detained in the town of Kerman in southeast Iran after authorities spent months tracking him down, the semi-official ISNA news agency said.
The suspect is accused of meeting four British intelligence operatives and giving them information.
Dadkhoda Salari, head of the Kerman revolutionary court, said: "Through the efforts of Iranian security forces, an MI6 spy has been arrested.
"He has met British intelligence officers in person 11 times, both inside the country and abroad, and provided them with intelligence."
It has not been suggested the alleged spy is a Briton, and Tehran has a history of announcing the arrest of people it claims are spying without releasing more details.
But the news is potentially embarrassing at a time when diplomatic relations between the UK and Iran had been improving after a two-year freeze.
On Friday, Iran's new envoy to Britain, Hassan Habibollah-Zadeh, held talks in London on his first visit since his appointment in November.
And a British diplomat, non-resident charge d'affaires Ajay Sharma, said he had "detailed and constructive discussions" about the UK's relationship with Iran during talks earlier this month.
He visited the site of the UK's embassy in the Iranian capital to assess the damage caused when it was ransacked by a mob in 2011, an incident which prompted the Government to pull its staff out of the country.
The thaw in relations between Tehran and the international community has also seen a deal reached over its nuclear programme.
Responding to the reported arrest a Foreign Office spokesman said: "We don't comment on intelligence matters."
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