Chowdhury is the eldest son of Azizur Rahman Chowdhury, the first Chief Editor of the Weekly Prekshit, and Sharifa Aziz Chowdhury. His native village is Katihara of Lakhai, and he was born at Kulikunda of Nasirnagar. Chowdhury spent his childhood in the Sylhet District.
Chowdhury received his 'Masters in Mass Communication and Journalism', and graduated in Political Science from the University of Dhaka. Mukhles Chowdhury achieved distinction in a research course in the King's College, University of London, under King's-UNHCR Scholarship.. He completed two research courses in Arabic for Quran in the University of Westminster and also studied in Royal Holloway and Birkbeck, University of London. Chowdhury took two Research Courses in London School of Economics and Political Science or LSE and studied for a PhD in Politics at Sheffield University in Britain.
In 1985 Chowdhury joined the Dainik Patrika, the newspaper which started on 31 January 1986, as the chief reporter. In early 1989 he switched over to the Dainik Naba Avijan and returned to the Dainik Patrika at the end of the year. Since 1981 he has been serving journalism with writing in various press including Dainik Bangla, Dainik Desh, Bichitra, Robbar, Sunday Express, Holiday and Khoborer Kagaj. In January 1991, he became special correspondent for the Ajker Kagoj. In September 1991 Chowdhury became the diplomatic editor and special correspondent of the Dainik Dinkal
In 1993, he became the Bangladesh correspondent for the Island Upali newspapers of Sri Lanka. He served as Editor of the Weekly Sarak, the Weekly Prekshit and the magazine Sromo.
In 2004 Chowdhury was appointed as press secretary and spokesman by President Iajuddin Ahmed, serving from December 2004 to November 2006. When Iajuddin took on the responsibility as Chief Advisor in 2006, he appointed Chowdhury as one of his advisors.
On 13 November 2006, President Ahmed, Chief Advisor of the Caretaker Government, appointed Chowdhury as the Senior Advisor to President with the rank and status of a Minister of State. From November 2006 to January 2007, when an acute national political impasses arose in Bangladesh out of uncertainty about Parliamentary elections, he performed the role of President’s special envoy in the negotiation process. He tried to reconcile issues between the two opposition leaders, Begum Khaleda Zia of the Bangladesh Nationalist Party, and Sheikh Hasina of the Awami League.
On 23 December 2006, the political parties agreed to participate in parliamentary elections in January. On the day all political parties joined the 22 January 2007 parliamentary election. Following that negotiation, they requested to extend last day of nomination for two days, as Presidential Adviser accepted this for smooth organizing the national election, while the AL and its Grand Alliance started submitting more new nomination papers for their candidates on 26 December 2006 as they changed some candidature in some areas in changed scenario. But on 3 January 2007, the last possible date, the Awami League and its Grand Alliance withdrew from elections when the Jatiya Party's Hussain Muhammad Ershad's nomination was cancelled..
A coterie using a judge gave a sentence to Jatiya Party (JP) Chairman H M Ershad. Agitating political parties stood by this move saying this was unacceptable at this election period. They chanted slogan: 'No Ershad, No Election' terming the court order motivated. Erstwhile State Minister for Home Lutfuzzaman Babar played role in cancelling Ershad's 5 nomination papers. For this, he called Returning Officers of 5 constituencies, Additional Divisional Commissioner of Dhaka and 3 Deputy Commissioners (DC) of the country, where the JP Chairman stood for election. Babar was lenient to Tarique Rahman thus Khaleda Zia. Meanwhile, he changed his allegiance to then Army Chief and engaged himself in dubious role, which was unknown to his former bosses. Presidential Adviser Mukhles Chowdhury tried to make Khaleda Zia understand that what he succeeded in bringing the AL and Grand Alliance to ensuing parliamentary election after a long parley and meeting many demands, now with this short cut process outside power will jeopardized the election. She did not realize the gravity of situation as her son was adamant on this. Ironically, then BNP had given charge to Babar for political contact with Ershad. At one stage, Babar and Tarique met Ershad. Finally, they both brought Ershad to Khaleda Zia at her cantonment residence while JP joined 4 Party Alliance for second time. Prior to 2001 parliamentary election, the JP first joined the 4 Party. Ershad deserted BNP before 2007 planned election saying Tarique became obstacle to give JP's demanded seats to contest forthcoming election being part of the alliance. The Army with DGFI worked availing advantage on prevailing situation in favor of Ershad, their former Chief. As Ershad claimed that upon receiving threats, he did hide in safe area in Gazipur. After three days he came out in a broad day light and joined 14 Party Alliance's public meeting in Dhaka. Col. Oli Ahmed floated new political party Liberal Democratic Party on 26 October 2006, where DGFI's role was evident. Then B Chowdhury's Bikalpa Dhara was amalgamated in LDP. But later both Chowdhury and Ahmed's parties saw divisions again. Then they all joined the AL led 14 Party alliance and named it Grand Alliance. In the meantime, the Army Chief Moeen U Ahmed with his vanguards MSP Aminul Karim, Brigadier General A T M Amin and Brigadier General Fazlul Bari had been working seriously to capture the power. On the other hand, Adviser Mukhles Chowdhury then tried utmost against that army group to save democracy, but the top politicians did not understand the situation.
Then Chowdhury used good offices of the western diplomats led by the US Ambassador Patricia A. Butenis and stopped the Martial Law while the army group had to retreat to the option of the state of emergency, which was supported by all political parties for their own interests. Khaleda Zia with Moeen's support on 29 October 2006 made all the papers of the state of emergency. However, Mukhles Chowdhury stopped the declaration of the emergency at night when the President Dr. Iajuddin Ahmed took over as the CA. Chowdhury was arguing through declaration of emergency the Army Chief would take over power. The AL led alliance was supporting the emergency from the beginning. At this stage, President Iajuddin declared a state of emergency on 11 January and postponed the elections under the pressure of Moeen and his army group,. as they would not be valid without full participation of the parties A group of military officers intervened to ensure stability, in what became called "One-Eleven." They established an interim government.
During 1994-1995, Bangladesh had a similar political deadlock, when the Awami League boycotted the 15 February 1996 election because no caretaker government had been established. In that event, negotiations had been led by the then-Commonwealth Secretary General Chief Emeka Anyaoku's special envoy Sir Ninian Stephen.
The violence and crisis in Bangladesh received international media coverage. In December 2006, WikiLeaks leaked documents from Chowdhury's mission with diplomats, including Patricia A. Butenis, as well as politicians and other stakeholders on solving Bangladesh's political impasses, when they had worked together during the volatile political situation in 2006-07 period. The caretaker government struggled to hold elections within the constitutional 90-day deadline. The dates for the scheduled election were changed to 21 January, then 23 January, and finally 22 January 2007 in efforts to accommodate the political parties.
Chowdhury had a series of meetings with stakeholders on governance and politics. With the help of United States envoys, Chowdhury stopped the imposition of martial law planned by General Moeen U Ahmed and his associates. They argued that they wanted to ensure the stability of the country because of the adverse effects of the political unrest on the society and economy.
Mukhles Chowdhury later said that General Moeen, Army Chief, was the main force in the military intervention and declaration by President Iajuddin Ahmed of a state of emergency on 11 January 2007. He started speaking against army-backed government on 12 January and his interviews were published by the Manabzamin, Naya Diganta and Amader Shomoy. According to Amar Desh reporting in 2009, Chowdhury said that Moeen had intended to capture the country's presidency through the interim Caretaker Government headed by Fakhruddin Ahmed, formerly with the World Bank. Aminul Karim united army dissident groups and also used Gen. Masud and Brig. Bari to achieve this. The main motto of Moeen, Aminul Karim and A M Amin was to make Moeen President of the country.
"Military coup in Bangladesh: Dateline 2007", one of his fact-finding write-ups about the One Eleven conspiracy, was published in the weekly Akhon Samoy of New York. Minister Mukhles Chowdhury revealed untold facts about 2007 military intervention in Bangladesh in interviews taken by media that include the Bangladesh Pratidin, the Daily Kaler Kantha, and the Daily Sun..
Chowdhury resigned under pressure after being the last advisor to President Iajuddin Ahmed, At the time, there had been reports that Chowdhury had become the de facto President and Prime Minister. Investigations confirmed that he had managed with integrity during this period. while Moeen U Ahmed was the unlawful authority of Bangladesh, who gave his promotion and extension in his army service.
Presidential Advisor and Minister Mukhles Chowdhury's success stories include he managed publishing two historic books from the statecraft making them above controversy for which he made top politicians understand that these two historic books have to be above all for the greater interest of the country so that with the passage of governments it remains intact. While the President of Bangladesh was in coma and was admitted in Dhaka Combined Military Hospital (CMC) and also in Singapore Mount Elizabeth Hospital, he did run the presidency keeping it on the right and single track while also stopping overdoing and attempt of overthrowing the President from the power. Last, but not least, Chowdhury brought all the political parties including agitating Grand Alliance in the parliamentary election of 22 January 2007 after having series of meetings with them and meeting their demands. As a result, the Grand Alliance was in that election from 23 December 2006 to 3 January 2007. Chowdhury was fighting against Moeen and Aminul Karim's group as they were making army deployment of Caretaker Government (CTG) dysfunctional in November 2006, managing 4 Advisors resignation in December 2006 what he was also able to replace and stopping Martial Law and the State of Emergency until 11 January 2007. Then Moeen was behind all power.
Mukhlesur Rahman Chowdhury has been the Chief Editor of the Bangladesh Worldwide and the Editor of the Weekly Prekkhit.. Veteran Journalist cum academic Mukhles Chowdhury has been Senior Editor of Birkbeck Law Review. He was the first Joint Secretary General of Commonwealth Journalists Association (CJA), Bangladesh.
In December 2003, Mukhles Chowdhury was elected President of the Overseas Correspondents' Association Bangladesh-OCAB (Foreign Journalists Association) for 2004 period.Hundred Years of Bangabhaban and Bangabhabaner Shatabarsha were published from Bangabhaban, where Chowdhury was the publisher, as the head of press wing of President's Office.
His two books, Samakalin Sangbadikata (Contemporary Journalism) and Protocoler Nigor (Bindings in Protocol), were published in 2005.
Mukhles Chowdhury's research articles were published in the South Asia Journal and LISA Journal.
His interviews were broadcast in NTV, in Channel I Europe, Takveer TV and LBTV24. His interview was published in the Dailiy Ittefaq.
Mukhlesur Rahman Chowdhury wrote for Counter Currents Magazine.
A frequent traveller Chowdhury visited the USA, the UK, France, Italy, the KSA, Nigeria, Japan, Thailand, Sri Lanka, Germany, India, Spain, Pakistan, Nepal, Vatican City, Myanmar as both official and personal capacities. He attended the UNGA, the SAARC, SID, CJA Conferences and also joined the Golden Jubilee of the United Nations in 1995.
A strong believer and Allah fearing statesman Mukhles Chowdhury performed Hazz in 2013 and also performed Umrah in 2004, 2006, 2010, 2016 and 2017.