Holmes was educated at Emmanuel College, Cambridge (part of the University of Cambridge), as well as Northern Illinois University and the University of Reading. In 1964, he enlisted in the Territorial Army, the part-time volunteer reserve of the British Army. Two years later he gained his commission, eventually rising to the rank of Brigadier. He spent most of his Territorial Army career with the 5th Battalion, The Queen's Regiment, a NATO-centred infantry battalion.

Between 1969 and 1985, he was a lecturer at the Department of War Studies at the Royal Military Academy Sandhurst, becoming Deputy Head of the Department in 1984. He was promoted acting Captain in 1972, substantive Captain in 1973, acting Major in 1978, awarded the Efficiency Decoration (TD) in 1979, promoted to substantive Major in 1980 In 1983 he transferred to and took command of the 2nd Battalion, The Wessex Regiment. He was promoted to Lieutenant-Colonel when he chose to give up full-time service in 1986. In the 1988 Queen's Birthday Honours, he was appointed Officer of the Order of the British Empire (OBE) (Military Division). He was promoted Colonel on 29 January, 1989.

In 1990, he became Director of Cranfield University's Security Studies Institute at the Royal Military College of Science, Shrivenham. In June 1991 he was appointed Aide-de-Camp to the Queen, holding the post until February 1997. In January 1994 he was appointed Honorary Colonel of the Southampton University Officer Training Corps, and in that February, he was appointed Brigadier TA at Headquarters Land Command. In 1995, he became Professor of Military and Security Studies at Cranfield.

From 1997 until his retirement in 2000, Holmes was Director Reserve Forces and Cadets, as well as having the distinguished honour of being Britain's senior serving reservist. In the 1998 New Year Honours he was promoted to Commander of the Order of the British Empire (CBE) (Military Division). From September 1999 — 1 February 2007, he was Colonel of the Regiment of the Princess of Wales's Royal Regiment (successor to The Queen's and Royal Hampshire Regiments). On 19 September, 2000 he was awarded the Volunteer Reserves Service Medal.

Holmes is also president of the British Commission for Military History and the Battlefields Trust, patron of the Guild of Battlefield Guides, chairman of Project Hougoumont, member of the Board of Trustees of the Royal Armouries, and a vice president of the UK National Defence Association. He has received the Order of the Dannebrog and holds honorary doctorates from the universities of Leicester and Kent. Holmes lives in Hampshire with his wife and two daughters. In his spare time he sits as a Justice of the Peace for North-East Hampshire.

Holmes has written over a dozen books, from Firing Line to Redcoat and was also editor in chief of the Oxford University Press' Companion to Military History. His television works include documentary series on the American Revolution such as Rebels and Redcoats in 2003 and Battlefield, a series concentrating on the bloody battles of World War II. His War Walks television series has been regularly repeated on British terrestrial and digital television channels, including BBC Two and UKTV History. One of his most noted documentary series was The Iron Duke, in which he chronicled the Duke of Wellington's life, travelling to India, to Waterloo and numerous other locations. In the BBC poll to find the 100 Greatest Britons in 2002, he presented the programme on Oliver Cromwell.

He used a similar format in his series, In the Footsteps of Churchill, a documentary on Winston Churchill. In this, he travelled across the world, including South Africa, Sudan, Egypt and various locations in the United Kingdom and Europe. He also wrote a book to accompany the series. Both the book and the television series have received much critical acclaim. With John Keegan Holmes also developed the BBC documentary Soldiers, a history of men in battle.