Dr. Chowdhury was the founding director of the research and evaluation division and the founding dean of the BRAC James P. Grant School of Public Health at BRAC University (JPGSPH). He was also previously the vice-chairperson of BRAC. Dr. Chowdhury is currently an advisor to JPGSPH and a member of the Advisory Council of the BRAC Institute of Governance and Development at BRAC University.
Dr. Chowdhury is a founder of the civil society watchdogs Bangladesh Education Watch and Bangladesh Health Watch. He is also the Co-Chair of the Bangladesh Water Multisectoral Partnership. Besides these, he is a board- and committee member of several organizations and initiatives both in Bangladesh and internationally. Previously, he was also a coordinator of the UN Millennium Task Force on Child Health and Maternal Health, set up by the former Secretary-General Kofi Annan.
He has a wide interest in development, particularly in the areas of education, public health, poverty eradication, and the environment. Dr. Chowdhury has published books and more than 150 articles in a variety of peer-reviewed international journals.