Air Commodore Simon Strasdin, UK Air Component Commander to the Middle East, said the latest strike on IS was made after militants came into contact with Iraqi Security Forces in northern Iraq.
After coming under fire, the Iraqi troops called for support from international coalition forces and two RAF Typhoons were deployed, the Ministry of Defence (MOD) said.
The jets then dropped two Paveway IV precision-guided bombs, the MOD added.
In an exclusive interview, Air Cdre Strasdin said it was "a direct strike" against the fighters who were "shooting at Iraqi forces".
"And that's really why we're there, we're there to support the Iraqis as they take ever-increasing control of Iraq," he said.
Jets based at RAF Akrotiri in Cyprus have been flying missions against IS, sometimes referred to as Daesh, for seven years as part of Operation Shader – the UK's contribution to the fight against IS in Iraq and Syria.
"Our role is to support the Iraqi forces, as they continue to stabilise and secure their country," Air Cdre Strasdin said.
It has been just over two years since former US President Donald Trump claimed all territory held by IS in Syria had been "100%" eliminated.
However, a report published in December last year said IS was still "driving" the UK's terror threat.
Air Cdre Strasdin told Forces News although "Daesh are defeated territorially, there are still pockets that are out there".
However, he said the group is "definitely in retreat".
"The threat that they pose to Iraq and to the wider globe in their ability to export terrorism is reducing," he said.
"Really, the message to Daesh is that there is nowhere to hide.
"So, whilst you remain on the run and you potentially pose a threat to us, we're watching, we're understanding, we're working closely with the Iraqi government and there is genuinely nowhere to hide.
"We will not rest until we've rooted you out of even those most remote places where you attempt to hide."
The air strikes by the Typhoons come after the RAF helped to clear an IS stronghold in northern Iraq in March.
The RAF supported Iraqi Security Forces ground operations during the 10-day mission.