In April 1999, he was promoted to Lieutenant-General and shifted as Adjutant-General (AG), Pakistan Army Generals Headquarter (GHQ). In October 2001, he was made "Corps-commander" of XI Corps, and served as the Commander of Western Military Command. During his military career, he was the leading and most experience general who served under General Pervez Musharraf Administration. Following the collapse of Taliban regime in Afghanistan, Aurakzai was made the commander of Western Military Command. As commander, he oversaw the extensive military operations led by the United States special operations forces. He responded with deploying hundreds of Mountaineering and Infantry battalions to guard the Pakistan-Afghanistan border, many of whom were redeployed as a result of the 2001 Indian Parliament attack.