The Hawk aircraft crashed at the air base on Anglesey Island in North Wales.
Photos purporting to be of the scene showed a large cloud of smoke exploding from the ground, reaching dozens of metres high.
Others showed wreckage on the ground in the centre of an airfield.
The pilot’s condition is not yet known.
The Welsh Ambulance Service said it was called shortly before 1.30pm on Tuesday to reports an aircraft had crashed at RAF Valley in Holyhead.
A spokesman said they sent an emergency ambulance to the scene and Wales Air Ambulance was also in attendance.
Sky News Defence Correspondent Alistair Bunkall said it is believed the aircraft was a two person plane.
We are aware of an incident today at RAF Valley involving a Hawk aircraft. We are investigating the incident.
— Ministry of Defence (@DefenceHQ) March 20, 2018
An eyewitness said they saw someone parachute form the plane just before it crashed.
Sian Williams told the Daily Post: “I was sat at Rhosneigr train station waiting for the train and you can see the airfield from there.
“I was watching the Red Arrow flying because you hardly ever see them and then it looked like it was about to land. Then, next thing I saw was the parachute and then the plane hit the runway and went up in flames.”
The RAF is asking anybody with photographs of the incident to send them in to help with an investigation.
Following the aircraft incident at RAF Valley earlier this afternoon, if you were an eyewitness, please send any photographs of the incident to [email protected] Any images may help with an investigation. Please DO NOT share these online. Please be sensitive, thank you.
— Royal Air Force (@RoyalAirForce) March 20, 2018
Prince William served with the RAF’s Search and Rescue Force at the Anglesey air base for three years.
RAF Valley is used as a training base for Hawk aircraft, which is the jet used by the Red Arrows team.
Bunkall added: “The Red Arrows are located at RAF Scampton during the summer season but during the off-season they train at various bases across the UK, including RAF Valley.”
The Red Arrows are the RAF’s aerobatic display team which performs at summer events, including the annual Trooping The Colour ceremony in London which the Royal Family watches from the Buckingham Palace balcony.
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Famous for their red, white and blue vapour trails, impressive stunts and trademark diamond formation, they are a familiar sight at air shows and military parades.
In 2011 two Red Arrows pilots died – one when their jet crashed after taking part in an air show and another when the pilot was ejected from his aircraft while it was on the ground.