Born in Prague he was the son of the diplomat Tomas Masaryk, who would become the first president of Czechoslovakia and the American born Charlotte Garrigue. Masaryk was educated in Prague and also in the US. He returned home in 1913 and served in the Austro-Hungarian army during WWI. He joined the diplomatic service and he was made charge d' affair to the USA in 1919, a post he held until 1922. In 1925 he was Ambassador to Britain. His father resigned as President in 1935 and died two years later, he was succeeded by Edvard Benes.
In September 1938 the Sudetenland of Czechoslovakia was occupied by German forces and Masaryk resigned as Ambassador in protest, although he remained in London. Other government members including Benes also resigned. In March 1939 all of Czechoslovakia was occupied and the Czech government in exile was established in Britain in 1940, Masaryk was made Foreign Minister. He regularly made broadcasts to occupied Czechoslovakia through the BBC during the war.
Masaryk remained Foreign Minister following the liberation of Czechoslovakia as part of the multi-party National Front government. The Communists under Klement Gottwald saw their position strengthened after the 1946 elections but Masaryk stayed on as Foreign Minister. He was concerned with retaining the friendship of the Soviet Union, but was dismayed by the veto they put on Czechoslovakian participation in the Marshall Plan. In February 1948 the majority of the non-Communist cabinet members resigned hoping to force new elections, instead a Communist government under Gottwald was formed. Masaryk remained Foreign Minister, although he was apparently uncertain about his action.
In March 1948 Masaryk was found dead in the courtyard of the Foreign Ministry. In the beggining of 2004 police concluded that he was murdered by his opponents, and that he did not commit a suicide as was ruled initially. Regardless, the circumstances of the assassination are still rather obscure.