He spent his early childhood in Kolkata and later his family settled in Dhaka. He was one of ten children born to his parents. After attending Nabakumar School at Bakshibazar, he studied at Dhaka College. He studied medicine at Dhaka Medical College, where he got involved with leftist political ideologies. As the general secretary of the Dhaka Medical College students' union, he held a press conference to expose the corruption at the hospital. After a turbulent student life, he finished his MBBS degree in 1964 and left for the UK for post-graduate studies in general and vascular surgery. In 1971, he fought for independence during Bangladesh Liberation War.
He was involved in setting up the 480-bed Bangladesh Hospital for freedom fighters and the refugees. The hospital was run by a team of Bangladeshi doctors, medical students and volunteers. Women with no previous training in healthcare were trained within days to help out the patients. This experience in the field hospital led him to believe that an effective healthcare delivery system can be developed in rural Bangladesh by training women as a primary healthcare delivery platform. This achieved worldwide credibility when it was eventually published in The Lancet.
In 1972 Dr. Chowdhury set up the Gonoshasthaya Kendra. Actually the idea was introduced in a concept paper titled, 'Basic Health Care in Rural Bangladesh' in Dhaka. The centre focuses on providing basic healthcare to the rural areas. The centre also runs a university, vocational training centre, agricultural cooperatives, hospital, a printing press, community schools and a generic drug manufacturing plant. Gonoshasthaya Kendra has been very successful in providing family planning services, lowering maternal, infant mortality rates. Though limited in its reach, it pioneered the introduction of cheaper generic drugs. In 1973, Gonoshasthaya Kendra introduced a Rural Healthcare Insurance System, the first of its kind in Bangladesh.
Critiques have pointed out that rather than being national, the centre's reach has been confined to specific areas. However, Zafrullah Chowdhury believes that public health is a state matter, it can never be left to the private sector.
Dr. Chowdury gained prominence by being the driving force in formulating the Bangladesh National Drug Policy in 1982. Before that, 4,000 commercial drugs were available in the market, mostly manufactured by the multi-national companies or imported from abroad. Most of the drugs were out of reach for majority of the people. Some of these drugs were unnecessary and even dangerous whereas the most essential 150 remained in short supply.
National drug policy changed all that. Following WHO guidelines for the developing countries, the policy restricted manufacturing and import of number of drugs to 225. It emphasised on manufacturing of generic drugs and manufacturing them locally. The result has been the wider availability of drugs at drastically reduced prices. And today, Bangladesh has turned into a drug exporting country.
In 2015, the International Crimes Tribunal, which was set up to try perpetrators of war crimes committed during Bangladesh Liberation War in 1971, charged Zafrullah Chowdhury on charge of contempt of court and sentenced him to "one hour" of 'confinement in the dock inside the courtroom" and fined him 5000 taka. The court found guilty of contempt of court for his statement expressing concern over British journalist David Bergman's conviction. This came as a surprise to many as being a freedom fighter, he was one of the vocal supporters of the controversial tribunal.2010 – International Public Health Heroes Award, UC Berkeley, US
1977 – Independence Day Award, Bangladesh
1992 – Right Livelihood Award, Sweden
1985 – Ramon Magsaysay Award for Community Leadership, Philippines
1974 – Swedish Youth Peace Prize