The photographs show the devastation caused after American Airlines flight 77 into the side of the building, killing 184 people - including all 59 passengers and crew on board.
Images show first responders battling stubborn blazes at the complex, debris from the plane's fuselage and haunting images from the scorched interior of the Arlington, Virginia landmark.
The airliner’s wings clipped off light poles before hitting into the western side of the building at the first-floor level. The jet ripped a hole in the structure that extended more than 100 yards into the building. It took firefighters days to fully extinguish the blaze.
Luckily, the plane struck a portion of the building that was under renovation and relatively empty. If it had struck another side or happened after the renovations were completed, the death toll would have been significantly higher, experts said at the time.
One haunting image shows a fireman holding the US stars and stripes flag in the gutted building while others survey the devastation.
The batch of 27 archived images uploaded to the website, FBI Records: The Vault also show fragments of the plane, which had left Dulles International airport in Washington DC for Los Angeles before it was hijacked by terrorists.
The plane which struck the Pentagon at 9.37am was the third of the four attacks and happened 30 to 45 minutes after the attack on the World Trade Centre towers in New York were hit, with the fourth plane - United 93 - aimed at Washington DC, crashing Pennsylvania shortly after 10am after passengers and crew fought to regain control.
One of the pictures of the aftermath of the Pentagon attack shows rescue workers with sniffer dogs searching the rubble for survivors or bodies. Officers spent several days trying to recover bodies hidden within the debris.
The total number of people killed in the 9/11 attacks was 2,996, while more than 6,000 were injured, making it is the single worst act of terrorism in history.
It was previously thought that the images had been newly released because of a fresh date stamp. But FBI spokeswoman Jillian Stickels said the pictures were first posted online in 2011.
A technical glitch caused them to disappear from the site for an undetermined period of time, she added. They were restored in recent days to public view once the FBI learned they were missing, according to the FBI spokeswoman.