Fuller was born in Chichester, West Sussex and is the son of an Anglican clergyman. After moving to Lausanne with his parents as a boy, he returned to England at the age of 11 without them; three years later, at "the somewhat advanced age of 14", he began attending Malvern College and, later trained for an army career at the Royal Military College, Sandhurst, from 1897 to 1898. His nickname of "Boney", which he was to retain, is said to have come either from an admiration for Napoleon Bonaparte, or from an imperious manner combined with military brilliance which resembled Napoleon's.

Fuller was commissioned into the 1st Battalion of the Oxfordshire Light Infantry (the old 43rd Foot), and served in South Africa from 1899 to 1902. In the spring of 1904 Fuller was sent with his unit to India, where he contracted typhoid fever in autumn of 1905; he returned to England the next year on sick-leave, where he met the woman he married in December 1906. Instead of returning to India, he was reassigned to units in England, serving as an adjutant to the 2nd South Middlesex Volunteers (amalgamated into the 7th Middlesex during the Haldane Reforms) and helping form the 10th Middlesex, until he was accepted into the Staff College at Camberley in 1913, starting work there in January 1914.

Fuller had an occultist side that oddly mixed with his military side. He was an early disciple of English poet and Magician Aleister Crowley, and was very familiar with his and other forms of magick and mysticism. While serving in the First Oxfordshire Light Infantry he had entered and won a contest to write the best review of Crowley's poetic works, after which it turned out that he was the only entrant. This essay was later published in book form in 1907 as The Star in the West. After this he became an enthusiastic supporter of Crowley, joining his magical order, the A∴A∴., within which he became a leading member, editing order documents and its journal, The Equinox. During this period he wrote The Treasure House of Images, edited early sections of Crowley's magical autobiography The Temple of Solomon the King and produced highly regarded paintings dealing with A∴A∴ teachings: these paintings have been used in recent years as the covers of the journal's revival, The Equinox, Volume IV.

After this, contact between the two men faded rapidly. The front pages of the 1913 issues of the Equinox (Volume 1, NOS. 9 and 10), which gave general directions to A∴A∴ members, included a notice on the subject of Fuller, who was described as a "former Probationer"; the notice disparaged Fuller's magical accomplishments and warned A∴A∴ members to accept no magical training from him. However, Fuller continued to be fascinated with occult subjects and in later years he would write about topics such as the Qabalah and yoga.

During the First World War, Fuller was a staff officer with the Home Forces and with 7 Corps in France, and from 1916 in the Headquarters of the Machine-Gun Corps' Heavy Branch which was later to become the Tank Corps. He helped plan the tank attack at the 20 November 1917 Battle of Cambrai and the tank operations for the Autumn offensives of 1918. His Plan 1919 for a fully mechanised offensive against the German army was never implemented. After 1918 he held various leading positions, notably as a commander of an experimental brigade at Aldershot.

The United States Army modified Fuller's list and issued its first list of the principles of war in 1921, making it the basis of advanced training for officers into the 1990s, when it finally reconceptualized its training.

The Nine Principles involve the uses of Force (combat power). They have been expressed in various ways, but Fuller's 1925 arrangement is as follows:

After the war Fuller collaborated with his junior B. H. Liddell Hart in developing new ideas for the mechanisation of armies, launching a crusade for the mechanization and modernization of the British Army. Chief instructor of Camberley Staff College from 1923, he became military assistant to the chief of the Imperial General Staff in 1926. In what came to be known as the "Tidworth Incident", Fuller turned down the command of the Experimental Mechanized Force, which was formed on August 27, 1927. The appointment also carried responsibility for a regular infantry brigade and the garrison of Tidworth Camp on Salisbury Plain. Fuller believed he would be unable to devote himself to the Experimental Mechanized Force and the development of mechanized warfare techniques without extra staff to assist him with the additional extraneous duties, which the War Office refused to allocate. He was promoted to Major-General in 1930 and retired three years later to devote himself entirely to writing.

Fuller was a vigorous, expressive, and opinionated Writer of military history and of controversial predictions of the Future of war, publishing On Future Warfare in 1928. Seeing his teachings largely vindicated by the Second World War, he published Machine Warfare: An Enquiry into the Influence of Mechanics on the Art of War in 1942.

Fuller is perhaps best known today for his "Nine Principles of War" which have formed the foundation of much of modern military theory since the 1930s, and which were originally derived from a convergence of Fuller's mystical and military interests. The Nine Principles went through several iterations; Fuller stated that ...the system evolved from six principles in 1912, rose to eight in 1915, to, virtually, nineteen in 1923, and then descended to nine in 1925... For Example, notice how his analysis of General Ulysses S. Grant was presented in 1929.

After retirement, Fuller served as a reporter during the Italian invasion of Ethiopia (1935) and the Spanish Civil War (1936–39). On his retirement in 1933, impatient with what he considered the inability of democracy to adopt military reforms, Fuller became involved with Sir Oswald Mosley and the British Fascist movement. As a member of the British Union of Fascists he sat on the party's Policy Directorate and was considered one of Mosley's closest allies. He was also a member of the clandestine far right group the Nordic League.

During the Second World War, 1939-45, Fuller was under suspicion for his Nazi sympathies. He continued to speak out in favour of a peaceful settlement with Germany. Alan Brooke (in his war diaries, p. 201) comments that "the Director of Security called on him to discuss Boney Fuller and his Nazi activities", though Alan Brooke commented that he did not think Fuller "had any unpatriotic intentions". Although he was not interned or arrested, he was the only officer of his rank not invited to return to Service during the war. There was some suspicion that he was not incarcerated in May 1940 along with other leading officials of the BUF because of his association with General Edmund Ironside and other senior officers. Mosley himself admitted to "a little puzzlement" as to why Fuller had not been imprisoned.

Fuller spent his last years a deeply embittered man feeling that the wrong side had won the Second World War, a thesis most fully announced in the 1961 edition of The Reformation of War where he announced his belief that Hitler was the savior of the West against the Soviet Union, and denounced Churchill and Roosevelt for being too stupid to see this. Fuller died in Falmouth, Cornwall in 1966.