Dr. Chaudhry was the coordinator of the UN Millennium Task Force on Child Health and Maternal Health set up by former UN Secretary-General Kofi Annan. He is a co-recipient of the 'Innovator of the Year 2006' award from the Marriott Business School of Brigham Young University in the United States and in 2017, he received the 'Medical Excellence' award from the Chicago-based Ronald McDonald House Charities. Dr. Chaudhry has published over 150 articles in peer-reviewed international journals and has also received the 'Best Influential Book' award given by University Press Ltd. His biography “Amr Brak Jibon” was recently published Prothoma,
Dr. Chowdhury is the founder of Bangladesh Education Watch and Bangladesh Health Watch, two civil society watchdogs on education and health respectively. He is on the boards and committees of several organizations and initiatives, including BRAC University, Bangladesh Institute of Development Studies (BIDS), Social Marketing Company, London School of Economics and Management Sciences for Health (MSH).
Since February 2015 he has been a BRAC-designated Director of DBH.