Following the 1905 Russian Revolution he was arrested by Okhrana and was sent to Siberia. He escaped but he was returned to exile on two more occasions. After the Russian Revolution he became the head of the Marx-Engels Institute in Moscow.

Lenin closed the Constituent Assembly in January, 1918. Soon afterwards all opposition political groups, including the Mensheviks, Socialist Revolutionaries and the Constitutional Democratic Party, were banned in Russia. Nicolaevsky remained active in politics and was arrested by the All-Russian Extraordinary Commission for Combating Counter-Revolution and Sabotage (Cheka) in 1921. The following year he was allowed to leave the country.

Nicolaevsky moved to Berlin and was involved in developing the Marx-Engels Institute in the city. Later he became the director of the International Institute of Social History in Amsterdam, repository of the archives of the Socialist International. During this period he associated with the Left Opposition. This included Lev Sedov, the son of Leon Trotsky, Victor Serge, Lilia Estrin, Henricus Sneevliet and Mark Zborowski. Together they published the Bulletin of the Opposition, the journal "which fought against Stalinist reaction for the continuity of Marxism in the Communist International".

Robert Service, the author of Trotsky (2009) has pointed out: "In November 1936 eighty kilos of Trotsky's archive was stolen from the International Institute of Social History at 7 rue de Michelet. The director of the Institute was Boris Nikolaevski. Despite being a Menshevik, he had earned Lev Sedov's trust by lending rare books to him and Trotsky. He was a devoted collector of all material that shed light on Russian revolutionary history and Lev had decided that his father's files would be safest in his care. The burglars left no sign of breakage on entry. The police were foxed.... Everyone suspected the NKVD but no one knew how the crime had been planned and undertaken."

Ignaz Reiss was an NKVD agent who had been in contact with anti-Stalin forces in Europe. He decided to defect but someone in the L betrayed him and after leaving a restaurant outside Lausanne on 5th September, 1937, a car pulled up bearing two NKVD agents, Francois Rossi and Etienne Martignat. One was driving, the other - holding a machine-gun. Reiss was shot seven times in the head and five times in the body. The assassins fled, not bothering to check out of the hotel in Lausanne. They abandoned the car in Berne. The police found a box of chocolates, laced with strychnine, in the hotel room. It is believed these were intended for his wife, Elsa Poretsky, and her son Roman.

Nicolaevsky decided to carry out an investigation to discover who the traitor was in the group. He approached another defector, Walter Krivitsky, and asked him for his views. Krivitsky suggested that Victor Serge was the traitor. We now know it was Mark Zborowski. As Gary Kern, the author of A Death in Washington: Walter G. Krivitsky and the Stalin Terror (2004), has pointed out: "Not satisfied with Krivitsky's abstract logic, Nicolaevsky pressed him to make a more specific report in short, to name his chief suspect. Krivitsky obliged in October 1938 with a personal letter to Nicolaevsky, again writing with painful deliberation and pedantic punctiliousness, but giving weighty reasons for suspecting Victor Serge. The verdict seems wrongheaded and even ironic today, in the light of what is known about Mark Zborowski, yet history has not completely cleared Serge of suspicion, despite apologies in the literature about his political lightheadedness and naive artist's indiscretion. Krivitsky points out that there was no other case in Soviet history of a man first arrested and imprisoned as a Trotskyist, then given not only his freedom, but also permission to travel abroad, all this at a time when other accused Trotskyists were suffering monstrous persecutions."

When the German Army invaded the Netherlands in May 1940, Nicolaevsky was forced to flee the country and soon afterwards managed to reach the United States. Over the next few years Nicolaevsky developed a reputation as the leading historian of the Soviet Union and became known as "the father of Kremlinology". For example, he was asked to study the testimony of the Soviet defector, Walter Krivitsky. Nicolaevsky argued: "Whom in his day did he not oversee; what secrets did he not hear! He told something about it in the press - beginning with his first articles.... and ending with his book... But what he printed does not convey the full store of information at his disposal. For his first publications he was obliged to choose separate sensational episodes out of his past. The more important part in his stories was not the episodes, but the overall picture of the whole organization and operation of Stalin's truly diabolical apparatus of secret organs."

Nicolaevsky and David Dallin co-authored Forced Labor in Soviet Russia (1947). Over the next few years Nicolaevsky developed a reputation as the leading historian of the Soviet Union and became known as "the father of Kremlinology". Other books by Nicolaevsky include Power and the Soviet Elite and Aseff the Spy.

Boris Nicolaevsky died in New York City on 21st February, 1966.