Doherty was born in Brisbane, Queensland, where he attended Indooroopilly State High School (which now has a lecture theatre named after him). He received his bachelor's degree in veterinary science in 1962 and his master's degree in veterinary science in 1966 from the University of Queensland. After obtaining his PhD in 1970 from the University of Edinburgh, Scotland, he returned to Australia to perform his Nobel Prize-winning research at the John Curtin School of Medical Research within the Australian National University in Canberra.

Doherty was elected a Fellow of the Royal Society (FRS) in 1987. He is the patron of the eponymous Peter Doherty Institute for Infection and Immunity, a joint venture between the University of Melbourne and Melbourne Health. It houses a group of infection and immunology experts, including Director Professor Sharon Lewin, who are charged with leading the battle against infectious diseases in humans. This became operational in 2014. He became an Honorary Fellow of the Academy of Medical Sciences in 2015.

Doherty's research focuses on the immune system and his Nobel work described how the body's immune cells protect against viruses. He and Rolf Zinkernagel, the co-recipient of the 1996 Nobel Prize in Physiology or Medicine, discovered how T cells recognise their target antigens in combination with major histocompatibility complex (MHC) proteins.

His semi-autobiographical book, The Beginner's Guide to Winning the Nobel Prize, was published by The Miegunyah Press, an imprint of Melbourne University Publishing Ltd, Melbourne in 2005. A Light History of Hot Air was published in 2007 by Melbourne University Press. In 2012 he published the book Sentinel Chickens. His fourth book The Knowledge Wars was published in 2015.

Viruses infect host cells and reproduce inside them. Killer T-cells destroy those infected cells so that the viruses cannot reproduce. Zinkernagel and Doherty discovered that, in order for killer T cells to recognise infected cells, they had to recognise two molecules on the surface of the cell – not only the virus antigen, but also a molecule of the major histocompatibility complex (MHC). This recognition was done by a T-cell receptor on the surface of the T cell. The MHC was previously identified as being responsible for the rejection of incompatible tissues during transplantation. Zinkernagel and Doherty discovered that the MHC was responsible for the body fighting meningitis viruses too.