Khandker served as a diplomat during his service days and was the Deputy Chief of Staff of Mukti Bahini during the Bangladesh Liberation War.

Khandker was posted in the Pakistan Air force Base in Dhaka as Second-in-Command when the Liberation War began in 1971.

[citation needed] He defected with Wing Commander M. K. Bashar and several other pilots in May 1971 and reached India.

He closely interacted with the senior officials of the Indian Eastern Command located at Fort William, Kolkata about training strategies for the Freedom Fighters as well as for overall operation.

The Bangladesh Air Force with its limited manpower and resources of only 09 officers, 57 airmen, and 03 aircraft carried out significant numbers of operation against the Pakistani invaders.

He received the gallantry award of Bir Uttom in 1972 for his luminous role in the Liberation War.

During the tenure of the immediate past Government of 2001–2006, Khandker is credited as the main architect of establishing the "Sector Commanders Forum"[6] by organising Sector and Sub-Sector Commanders of the liberation war that waged strong movement against pro-Jamat and other alleged war criminals.

In 2014, Khandaker wrote his memoirs "1971 Bhetore Baire" (1971: Inside and Outside) and was praised by historian Sirajul Islam who said that "the book provided a balanced presentation of history and the outline of the war and the interest of different vested groups surrounding the war came up in it.

[9] However, it drew ire from the ruling Awami League government, for creating "distorting historic facts" the history of the Bangladesh Liberation War, as he wrote in his book that Sheikh Mujibur Rahman ended his 7 March speech with "Joy Pakistan.

"[10] He further added that Sheikh Mujib did not declare independence from 7 March until his arrest, did not leave any written notes or recorded voice messages and did not go through any predefined directions.

Yahya Khan realized that if Bangabandhu declared independence on March 7, the movement could not be controlled in any way.

On the day of the March 7 speech, the situation inside the cantonment was quite normal, everyone was busy with their work.

If the Awami League leaders had a war plan, the people and government, private and military officials could have been properly organized in a short time from the beginning of March.

In addition to the meeting between Tajuddin Ahmed and Sheikh Mujib on the evening of March 25, Maidul Hasan, in a discussion between Maidul Hasan, Wing Commander SR Mirza and me on the topic of "Pre-Liberation War: Conversation", said: He did not discuss the decision with anyone at the helm of the party.

"Mr. Tajuddin further said that after giving the draft declaration to Sheikh Mujibur Rahman, he did not read it and remained unanswered.

Later, Maidul Hasan asked the Awami League's publicity secretary Abdul Momin about this.

Abdul Momin said that when he was entering Bangabandhu's house, he saw Tajuddin Ahmed carrying files in his armpit with a very angry look.

[11] An uproar in parliament ensued where Awami League lawmakers demanded that the book must be banned and its copies will be confiscated.

They also demanded filing a sedition case against the writer, who is also a sector commander of the liberation war.

[12] Awami League lawmaker Sheikh Fazlul Karim Selim said that the book "has distorted historic facts and violated the country's constitution by giving such misleading information on Bangabandhu.

""I am in doubt whether he wrote the book by taking huge amount of money from any agency," he added.

[12] Mohammed Nasim said "Bangabandhu Sheikh Mujibur Rahman awarded AK Khandaker with the Bir Uttam honours but he (Khandaker) insulted the father of the nation by extending his support to Khondaker Mostaq Ahmad.

[14] He was then declared a persona non grata in the district of Gazipur and pro-government lawyers demanded withdrawal of all of his titles.