Chowdhury was the joint secretary of Cabinet Division in 2017.[8] In 2018, he was the Sylhet Divisional Commissioner.[9]
In February 2020, Chowdhury was transferred from additional Secretary to Appointment Promotion and Deputation Wing of Ministry of Public Administration to Secretary of the Ministry of Shipping.[10] Chowdhury launched an alternate ferry service for the Shimulia-Kathalbari route on an experimental basis.[11] He suggest using waterways to trade with India to reduce costs.[12][13] He advocated using the India-Bangla protocol routes under Bangladesh Inland Water Transport Authority and highlighted the opportunity for Bangladesh to trade with the Seven Sister States of India.[14][15] He was present in negotiations with the Water transport workers which led to the strike ending.[16][17] He reported that a ferry hit the pillar of the Padma Bridge due to negligence of the crew.[18] He was present at the 2.34 billion BDT contract signing between Chattogram Port Authority and Nippon Koei JV.[19]
On 27 October 2022, Chowdhury was promoted to senior secretary.[5][27] On 31 October, he was transferred from the Local Government Division to the Ministry of Public Administration replacing KM Ali Azam.[5][28] He launched the Government Employee Management System for the public administration.[29] According to The Daily Star, he oversaw significant changes in the public administration postings to advantage the Awami League led government before the general election in 2024.[30]
Mokhlesur Rahman replaced Chowdhury as the Senior Secretary of the Ministry of Public Administration.[31] After retirement, Chowdhury sought nomination for the Bhola-4 constituency from Awami League ahead of the general election in 2024.[32] He was made an officer on special duty after the fall of the Sheikh Hasina led Awami League government and Md. Mokhlesur Rahman was appointed his replacement.[33]
