Khawaja gained commission in Pakistan Air Force in January 1971. He completed his aviation training to become an aviator of Alouette III, and was selected to be sent to PAF Special Warfare School. After his graduation in JUNE 1973, Khawaja as flying officer, was selected as a flight specialist. Squadron Leader Khawaja actively participated in Soviet–Afghan War along with elite Black Storks, also known as Special Service Group. In 1985, Squadron Leader Khawaja pursued his career to become an intelligence officer. After passing the selection exam, Khawaja joined ISI where he actively participated in Soviet–Afghan War. In 1987, former President and Chief of Army StaffGeneralZia-ul-Haq dismissed him from his position for his "outspoken views", a subsequent forced-retirement given by the Pakistan's Judge Advocate General Branch in 1987.
''Asia Times'' comments
A November 9, 2005, article in the Asia Times described Khawaja as the "point man" for Mansoor Ijaz, which it describes as "...a US citizen of Pakistani origin with close ties to the right wing of the Republican Party". The Asia Times says that Ijaz is negotiating a peace with the remaining elements of the Taliban, with Khawaja's assistance. The Associated Press names Khawaja a spokesman for a Pakistani human rights group named Defense of Human Rights.
A noted friend of the Egyptian-Canadian Khadr family, Khawaja spoke in their defence saying they were being unfairly targeted by Canadian authorities because of deference to the United States, and Islamophobia. He has also said that Canada is "selfish and self-centred" and deserves to be bombed by terrorists. Deborah Scroggins, author of the book , describes meeting Zaynab while she was a house-guest of Khawaja, in Islamabad, Pakistan, in 2004.
Arrest
Khawaja was arrested in Aabpara on January 26, 2007, on charges of distributing hate material, which he denied.
Death
He was found dead in Mir Ali on April 30, 2010 – a month after being kidnapped by a group calling themselves the "Asian Tigers", while filming a documentary about Colonel Imam. Imam, British journalistAsad Qureshi and Qureshi's driver Rustam Khan were also kidnapped with Khawaja. Qureshi and Khan were released in September 2010. Imam was killed in January 2011.