Two officials who spoke on the condition of anonymity told Reuters the operation took place in late September and was timed to affect Tehran’s ability to spread what they called propaganda.
One of the officials said the strike affected physical hardware, but did not provide further details.
The attack highlights how Mr Trump’s administration has been trying to counter what it sees as Iranian aggression without spiralling into a broader conflict.
Asked about Reuters reporting on Wednesday, Iran’s Minister of Communications and Information Technology Mohammad Javad Azari-Jahromi said: “They must have dreamt it,” Fars news agency reported.
The US strike appears more limited than other such operations against Iran this year after the downing of an American drone in June and an alleged attack by Iran’s Revolutionary Guards on oil tankers in the Gulf in May.
The United States, Saudi Arabia, Britain, France and Germany have publicly blamed the Sept. 14 attack on Iran, which denied involvement in the strike. The Iran-aligned Houthi militant group in Yemen claimed responsibility.
Publicly, the Pentagon has responded by sending thousands of additional troops and equipment to bolster Saudi defences – the latest US deployment to the region this year.
The Pentagon declined to comment about the cyber strike.
“As a matter of policy and for operational security, we do not discuss cyberspace operations, intelligence, or planning,” said Pentagon spokeswoman Elissa Smith.
The impact of the attack, if any, could take months to determine, but cyber strikes are seen as a less-provocative option below the threshold of war.
Tensions in the Gulf have escalated sharply since May 2018, when Mr Trump withdrew from the 2015 Joint Comprehensive Plan of Action with Tehran — otherwise known as the Iran Nuclear Deal — that put limits on its nuclear program in exchange for the easing of sanctions.
It was unclear whether there have been other US cyber attacks since the one in late September.
Reuters contributed to this report