Horner was raised in a military household; his father Murray Horner had served in New Guinea during World War II and later joined the Citizen Military Forces (CMF). He joined the Army after completing school in 1966 and attended Royal Military College Duntroon. Horner served in the Australian Army for 25 years, including active service in South Vietnam.

Horner was appointed to a position at the Australian National University's Strategic and Defence Studies Centre in 1990 and is currently Professor of Australian Defence History at the ANU's Research School of Pacific and Asian Studies. In 1998 he was described as "one of Australia's most respected military historians". In 2004 Horner was appointed the Official Historian and general editor for the Official History of Australian Peacekeeping, Humanitarian and Post—Cold War Operations, of which six volumes are planned. A team lead by Horner also won a tender to write the official history of the Australian Security Intelligence Organisation (ASIO) which Horner plans to cover in two volumes published in 2013 and 2015. Horner has written or edited 28 books and a further 75 journal articles, reports and chapters in books. For his "service to higher education in the area of Australian military history and heritage as a researcher, author and academic", Horner was appointed a Member of the Order of Australia in the Queen's Birthday honours list of 2009.

Horner's books include:

• High Command, Australia and Allied Strategy, 1939—1945, George Allen & Unwin, Sydney, in association with the Australian War Memorial, Canberra, 1982.
• Duty First: the Royal Australian Regiment in war and peace, Allen & Unwin, Sydney, 1990. A revised edition was released in 2008.
• The Gunners: A History of Australian Artillery, Allen & Unwin, Sydney, 1995.
• Inside the War Cabinet: Directing Australia's War Effort, 1939—1945, Allen & Unwin, Sydney, 1996.
• (with Desmond Ball) Breaking the Codes: Australia's KGB Network, Allen & Unwin, Sydney, 1998.
• Blamey: The Commander-in-Chief, Allen & Unwin, Sydney, 1998.
• Defence Supremo: Sir Frederick Shedden and the Making of Australian Defence Policy, Allen & Unwin, Sydney, 2000.
• The Australian Centenary History of Defence, Volume 4, Making the Australian Defence Force, Oxford University Press, Melbourne, 2001.
• Strategic Command: General Sir John Wilton and Australia's Asian Wars, Oxford University Press, Melbourne, 2005.