Sue Gray, 50, is only the second female two-star officer after she was promoted to the rank and appointed director of combat air at Defence Equipment and Support.
She follows Air Vice-Marshal Elaine West, 51, who became director of projects and programme delivery at the Defence Infrastructure Organisation in August.
Air Vice-Marshal Gray joined the RAF in 1985 after gaining a degree in electronics from Newcastle Upon Tyne Polytechnic.
She was commissioned into the Engineer Branch and later deployed to Iraq in the First Gulf War in 1991, and on Operation Telic in 2003 when she was chief engineer for the Joint Helicopter Force.
She will now be responsible for the procurement and maintenance of all combat aircraft, training aircraft and remotely piloted air systems for the armed forces.
Air Vice-Marshal Gray said: "It is an immense privilege to have served my country for the last 28 years in the RAF and I am delighted to continue to do this in my new role as director of combat air. I look forward to the challenges of ensuring the UK stays at the cutting edge of combat air power, delivering world-class fast jet training aircraft and remotely piloted air systems to our armed forces."
Defence minister Anna Soubry said: "I am delighted that the armed forces continue to demonstrate there are no glass ceilings for female personnel."