The Sun reports that Flight Lieutenant Ian Fortune, 28, had flown in to pick up casualties as a firefight raged between American and Afghan forces and heavily-armed rebels near Garmsir in Helmand Province.
Flt-Lt Fortune - who had TV presenter Mike Brewer on the aircraft filming a documentary - was advised to hold off on approach to the battle as it was "too hot" on the ground. He circled until troops reported incoming fire had calmed down.
But as he flew in the helicopter came under attack - which continued as casualties were being loaded.
Then, as he lifted off, Flt-Lt Fortune was shot. A bullet hit a metal rail on the front of his helmet which is used to attach night vision goggles.The round then penetrated his helmet hitting him between the eyes. It knocked his head back and caused severe bleeding.
More bullets followed, hitting the Chinook's controls and shutting down the stabilisation system.
But with blood pouring into his eyes, Flt-Lt Fortune battled with the controls to stop the chopper from spiraling out of control
Then with the aircraft lurching from side to side he continued flying for eight minutes before landing at Camp Bastion.
He was taken to the field hospital and treated for his wound.
It is the first time in the nine-year war in Afghanistan a pilot has been shot while in the air.
One senior RAF source said: "This could have become one of the worst incidents of the conflict.
"If the bullet had hit the pilot a millimetre lower, those on board wouldn't have stood a chance.
"And had it not been for the skill of the pilot the result would have been the same."
Brewer, 41, who was with a crew from the Discovery Channel, said: "The courage and heroism of the pilot was beyond belief.