The jet broke off into two pieces when it crashed at the airfield.
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The pilot ejected during the incident at the Mona airfield involving an RAF Hawk aircraft at 1225 BST.
He was the only person on board the two-seater jet and was flown to hospital in Bangor but later discharged.
An eye witness said he saw the pilot land in trees and his seat end up in a nearby field.
The RAF said it was investigating the cause of the crash.
The Hawk was on a routine flight to report on weather conditions in the area when the incident happened.
I looked out the bedroom window and saw the pilot was lying in a nearby field
Witness Dennis Morris
Dennis Morris, 68, who lives near the crash site, told the BBC News website he heard a noise "like a horrendous car crash with the screeching of metal".
Mr Morris said he saw the crashed jet broken in two.
He added: "I looked out the bedroom window and saw the pilot was lying in a nearby field.
"He wasn't moving at all - he appeared to be quite badly injured."
Four fire engines and three other vehicles have been deployed to Mona airfield, which is eight miles away from the RAF Valley base, by North Wales Fire and Rescue service.
The pilot was discharged after treatment at Ysbyty Gwynedd, Bangor
A spokeswoman for North Wales Police said initial reports suggested the pilot had ejected safely from the plane and landed in a field before it crashed.
Squadron Leader Mark Byrne, a spokesman for RAF Valley, said details of the pilot's injuries were not yet known.
He said: "I can confirm that a Hawk aircraft has crashed at RAF Mona, which is a small satellite airfield connected to RAF Valley.
"We will not speculate about the cause of the accident as an investigation will be carried out to establish what has happened."
BAE Hawk, similar to the one that crashed.
An RAF Hawk training jet has crashed at Mona Airfield on Anglesey Island in the United Kingdom. The crash occurred at 12:25 p.m. local time.

The pilot is reported to have ejected prior to the crash. No injuries are reported at this time.

"I can confirm that a Hawk aircraft has crashed at RAF Mona, which is a small satellite airfield connected to RAF Valley. One person was on board but we do not know the extent of the pilot's injuries at this time," said spokesman for RAF Valley, Squadron Leader Mark Byrne.

According to the U.K.'s Defense Ministry, the aircraft carries up to two pilots, but only one was on board the plane at the time of the crash.

The plane was put into service in 1976 for flying and weapons training. The T1 version of the Hawk is for training pilots in fast flying at an advanced level and the T1A Hawk is designed to train pilots to use weapons at an advanced level. It is also the aircraft used by the Red Arrows RAF display team.

Search and rescue personnel are on their way to the scene and an investigation is being launched. The wreckage of the plane is said to be in two pieces. It is not known what caused the crash.

"We will not speculate about the cause of the accident as an investigation will be carried out to establish what has happened," added Byrne.