Walker was promoted to group captain in 1997, and attended the Higher Command and Staff Course in 1999, before taking command of RAF Cottesmore and the UK Harrier Force. In 2001 he was posted to HQ No. 3 Group, spending most of that tour deployed overseas supporting operations in Afghanistan as part of Operation Enduring Freedom; he was appointed Commander of the Order of the British Empire in the 2002 New Year Honours. Promoted to air commodore in 2002, he took up the post of Assistant Chief of Staff J3 (Operations) in the Permanent Joint Headquarters, with responsibility for the management of all United Kingdom expeditionary operations, but with his main focus being Operation Telic, the United Kingdom's contribution to the Iraq War.