Choudhury joined the Pakistan Foreign Service in 1953. During his diplomatic career with Pakistan, he held various assignments in Rome, Baghdad, Paris, Lisbon, Jakarta and New Delhi. During the Bangladesh Liberation War in 1971, he defected to the Provisional Government of Bangladesh. He negotiated the recognition of Bangladesh by over 40 countries. On Victory Day, 1971, he addressed the Indian parliament on behalf of the Bangladeshi people. He became the first Bangladeshi Ambassador to the Federal Republic of Germany in 1972, with concurrent accreditation to Switzerland, Austria and the Holy See. He was also the first Permanent Representative of Bangladesh to the International Atomic Energy Agency (IAEA) and the United Nations Industrial Development Organization (UNIDO). In 1975, Choudhury sheltered Sheikh Hasina and Sheikh Rehana at his residence in Bonn after the assassination of Sheikh Mujibur Rahman.