RAF Wyton is commanded by a Wing Commander and is located in Huntingdon, Cambridgshire. It is a Joint Forces Command station and its main role is as Headquarters Joint Forces Intelligence Group (JFIG). JFIG units at RAF Wyton include:

• JFIG HQ;
• RAF Wyton HQ;
• Defence Geospatial Intelligence Fusion Centre (DGIFC);
• HQ Defence HUMINT Organisation (HQ DHO);
• 14 Squadron, 42 Engineer Regiment (Geographic); and
• 13 & 16 Squadron, 42 Engineer Regiment (Geographic) (arriving Summer 2014).

RAF Wyton also provides support and accommodation to various Lodger Units (LUs) including:

• Defence Security Assurance Services;
• Defence Infrastructure Organisation;
• Defence Intelligence Estates Rationalisation Team (PRIDE);
• 57 (Reserve) Squadron, No 3 Elementary Flying Training School;
• Cambridge University Air Squadron;
• University of London Air Squadron;
• No 5 Air Experience Flight; and
• Wyton Area Voluntary Band (WAVB).

While there is no longer any operational flying on the Station, RAF Wyton is home to a number of flying training units. These include: 57(R) Squadron, No 3 Elementary Flying Training School who provide basic flying training at Wyton for trainee pilots of the RAF, using the Grob Tutor aircraft. The aircraft are also used by the University of London Air Squadron and Cambridge University Air Squadron to provide basic flying instruction and air experience to University Cadets, and by No 5 Air Experience Flight for air experience flying of Air Training Corps cadets.

On 25 March 2013 the Ministry of Defence announced that all flying at RAF Wyton would cease by mid 2014.