Trounson introduced two world-first procedures which greatly improved the success rate of in-vitro fertilisation. They were the use of a fertility drug to induce multiple ova and the freezing of embryos for future use. These procedures enabled more than 300,000 women worldwide to conceive successfully. Trounson made headlines in 1980 with the first IVF birth in Australia and afterwards set up the Monash team of Wood, Trounson, Leeton, Talbot and Kovacs. He was appointed a Reader in the Department of Obstetrics and Gynecology in 1984 and the following year the Director of the Centre for Early Human Development. In 1991 he was appointed a Personal Chair in Obstetrics and Gynaecology/Paediatrics at Monash University and was awarded the Wellcome Medal. Further awards followed in 1994 and 1994 when he received the Patrick Steptoe Memorial Medal from the British Fertility Society, and the Benjamin Henry Sheares Medal from the Obstetrical and Gynaecological Society, Singapore. In 2000, he again made international headlines when he led the team which discovered that nerve stem cells could be derived from embryonic stem cells. This announcement led to a dramatic increase in interest in the potential of stem cells to cure a range of currently incurable diseases. In 2002, Tounson apologised for misleading members of the Australian Parliament by attributing the recovery of a crippled rat to embryonic stem cells, when in fact the cells were germ cells from a fetal rat. In 2003 he was appointed a Personal Chair as Professor of Stem Cell Sciences at Monash University, was awarded a Doctor Honoris Causa by the Faculties of Medical Sciences and Physical Education and Physiotherapy, Vrije Universiteit Brussel, Brussels, Belgium, and was named Australian Humanist of the Year. Trounson was the founder and executive vice-chairman of the National Biotechnology Centre of Excellence, Australian Stem Cell Centre, as well as Global Scientific Strategy Advisor. He serves on the Science Advisory Board of the Genetics Policy Institute and was a founder of the Australian Stem Cell Centre. In 2007 he was appointed President of the California Institute for Regenerative Medicine, a position he held until his return to Australia in 2014. In 2008 Trounson was inducted as an Honorary Member in the Monash University Golden Key Society.
