The patient, a 24-year-old man from Afghanistan, had complained of impaired vision in his right eye, headaches and a discharge from his right nostril.
Asked how the pencil had become lodged in his head, he said he only remembered a childhood accident about 15 years earlier where he fell and suffered a strong nosebleed.
A medical presentation on the 2011 case at Aachen University Hospital was presented at a conference in the western city of Essen this week.
Surgeons spotted the seven-centimetre (2.7-inch) pencil, which had lodged in the back of the throat and damaged the eye socket, in a Computerised Tomography (CT) scan.
After the surgery, the unnamed patient made a quick recovery and was released from hospital within days, the presentation says, although the man’s vision remained impaired.