Bubnov was born in Ivanovo-Voznesensk in Vladimir Governorate (now Ivanovo, Ivanovo Oblast, Russia) on 23 March 1883 into a local Russian merchant's family. He was expelled from Moscow University for revolutionary activities. He studied at the Moscow Agricultural Institute and while a student joined the Russian Social Democratic Labour Party (RSDLP) in 1903. He was a supporter of the Bolshevik faction of the party and attended the 4th (1906) and 5th (1907) Party Conferences in Stockholm and London, as well as the 1912 Prague conference. In 1909 Bubnov was made an agent of the Central Committee in Moscow and later sent to organize workers in Nizhny Novgorod. He also contributed to Pravda. He was arrested a total of thirteen times by the czarist government.
On the outbreak of the First World War Bubnov became involved in the anti-war movement. He was arrested in October 1916 and exiled to Siberia. Bubnov returned to Moscow in 1917 after the February Revolution. He joined the Moscow Soviet and, at the 6th Party Conference in July 1917, he was elected to its central committee. Just before the October Revolution, he was elected as one of the seven members of the first Bolshevik Politburo alongside Lenin, Zinoviev, Kamenev, Trotsky, Stalin, and Sokolnikov. As a member of the Military Revolutionary Committee he helped organize the October Revolution. During the Russian Civil War Bubnov joined the Red Army and fought on the Ukrainian Front and in the Caucasus. After the war he joined the Moscow Party Committee and became a member of the Left Opposition.
He was not always orthodox: The Party noted that he was with the "left-wing" in 1918, the "Democratic-Centralists" in 1920–1, and the Trotskyites in 1923, when he signed their Declaration of 46. In January 1924, however, he switched to supporting Joseph Stalin and was rewarded by being appointed as Head of Political Control of the Red Army. From the 13th (1924) to 17th (1934) Party Conferences, he was elected to the central committee.
Under the pseudonym Kisanko, he traveled to Guangzhou, China, to lead a team of Soviet advisors to the Nationalists, then in close cooperation with the Communists. Following the Canton Coup on 20 March 1926, he worked out an agreement with the new Nationalist strongman Chiang Kaishek. He was recalled at Chiang's request the next month. He then worked with Grigori Voitinsky and Fedor Raskolnikov on the "Preliminary Theses on the Situation in China", which was presented to the ECCI in November and December of that year.
In 1929, he replaced Lunacharsky as People's Commissar for Education. As Commissar for Education, he ended the period of progressive, experimental educational practices and switched the emphasis to training in practical industrial skills.
He was arrested by the NKVD during the Great Purge on 17 October 1937 and expelled from the Party Central Committee in November 1937. Records from the time, which were not made public until the 1980s and 1990s, show that he was sentenced to death on 1 August 1938 and shot the same day. The modus operandi of the Stalinist regime was often to keep secret the real disposition of particular purged persons: whether internally exiled to a labor camp, sent to a psychiatric hospital (in which the regime disguised confinement and drugging as compassionate "health care"), or executed. It encouraged their families and the general public to believe that they were probably still alive in a camp or hospital somewhere. Bubnov was posthumously rehabilitated in February 1956 during the de-Stalinization of the Khrushchev thaw. However, even at the time, the Soviet government did not make public the lists of the purged persons who had already long been executed. Thus, their relatives were often still searching for them in various psychiatric hospitals in the 1970s, as was the case with Bubnov.