John Christodoulou is a medical graduate of the University of Sydney, and has formal qualifications in paediatrics, medical genetics and genetic pathology, with his main focus of clinical practice being in the diagnosis and management of children with inborn errors of metabolism for over three decades. He has an active laboratory-based Rett syndrome research program, as well as in genetic metabolic disorders, particularly the mitochondrial respiratory chain (energy production) disorders, and has a strong research interest in the application of next generation sequencing technologies for disease gene discovery in rare Mendelian disorders. He was the Director of the Western Sydney Genetics Program at the Children's Hospital at Westmead, and the Head of the Discipline of Genetic Medicine at Sydney University until December 2015.

In 2016 he joined the Murdoch Children's Research Institute and established the Neurodevelopmental Genomics Research Group. At this time he also took up the inaugural Chair in Genomic Medicine at the University of Melbourne. The following year he and his long term collaborator Professor David Thorburn and decided to merge their research groups, and they now co-lead the Brain and Mitochondrial Research Group at the MCRI. in 2017 John became the Director of the MCRI's Genetics Research Theme.

John is a former Past President of the Human Genetics Society of Australasia (2005 – 2007). In 2010 he became a Member of the General Division of the Order of Australia (AM) and in 2017 became a Fellow of the Australian Academy of Health & Medical Sciences.