In late March 1941, when Yugoslavia signed the Tripartite Pact, Furlan was evacuated from the country with the help of the British intelligence service with which he had established a collaboration. After the Axis invasion of Yugoslavia and the Italian occupation of Slovenia, he was convicted to death in contumaciam by the Italian authorities. After a short stay in Palestine, Furlan travelled to the United States. Together with the liberal conservative Slovenian émigré politicians Izidor Cankar and Franc Snoj, Furlan propagated for the Yugoslav and Slovene cause. In 1942, he published a brochure titled Fighting Yugoslavia: The Struggle of the Slovenes, in which he articulated, among other, the Slovenian claims for the annexation of his native Julian March region to Yugoslavia. In 1943, he moved to London, where he served as Minister of Education in the exile government of Miloš Trifunović between June and August 1943. In the first years of the war, Furlan supported the Chetnik resistance movement of Draža Mihajlović, but after early 1944, he became supportive of Josip Broz Tito's Yugoslav Partisans. After the Yugoslav Prime MinisterIvan Šubašićrecognized the partisan movement in June 1944, Furlan replaced Alojzij Kuhar as the official Slovene speaker of the Yugoslav government in exile for the Radio London. In summer 1944, he had several speeches directed to the members of the collaborationist Slovene Home Guard, urging them to join forces with the partisan forces. One of his speeches, titled A Clear Word from London was printed on leaflets which were dropped by Allied airplanes over Slovenia. In Autumn 1944, Furlan replaced Izidor Cankar as Minister for Culture and Telecommunication in the Provisional Government. In early 1945, he went to the liberated territories in southern Slovenia together with Franc Snoj.
After the end of World War II, he became the dean of the Faculty of Law of the University of Ljubljana. He tried to maintain a critical attitude towards the Communist regime; among other things, he secretly translated George Orwell's Animal Farm. In June 1947, he was arrested and tried at the so-called Nagode Trial, together with 31 other liberal democratic and left-wing Slovene intellectuals, such as Črtomir Nagode, Ljubo Sirc, Angela Vode and Franc Snoj. Furlan was accused of having been member of a Masonic lodge in the 1930s, of having maintained contacts with the British intelligence since the late 1930s; the main accusation regarded his translation of Orwell's Animal Farm and his friendly relations with the American Red Cross official Jack Hoptner. In August 1947, he was sentenced to death. The sentence was later commuted to 20 years of forced labour. He was released on parole after four and a half years because of illness. In 1952, he moved to the small Upper Carniolan town of Radovljica to escape the daily intimidations to which he was subjected in the Slovenian capital. In November 1953, he was reportedly attacked by agents of the Yugoslav secret police, in which he suffered severe injuries. He died in Ljubljana or Radovljica at the age of 62 and was interred in the cemetery in the Vič neighborhood of Ljubljana.
Filozofske osnove pojma nevarnosti v kazenskem pravu
Politični nazor T. G. Masaryka
Socialna filozofija Anatola Francea
Problem pravne kavzalnosti
Racionalizem in revolucija
Other
In 1998, the Slovenian writerDrago Jančar wrote a short story about Furlan, titled "Joyce's Pupil". The story was in 2006. Boris Furlan was the father of the renowned physician Borut Furlan.