By the 1940s Harel joined the Haganah and the British auxiliary forces to fight the Nazis. He headed the intelligence branch of the Haganah in 1942. It was Harel who sank the Irgun ship the Altalena, upon orders given by David Ben-Gurion.
Harel quickly climbed the ranks of the Israeli elite, ultimately becoming the first head of the Shin Bet, Israel's internal security service. He was the Mossad director from 1952-1963, where he directed both the Shin Bet and the Mossad.
He is credited with developing a close relationship with the CIA and, together the United States, Israel collected information about the Soviet Union. He also created the Trident Network in which Israel, Iran, and Turkey collected intelligence about the Egyptian government.
Harel was known for his dedication to defending Israel and protecting democracy within the Jewish state. During his tenure as the Mossad chief, he led two famous operations. The first was the capture in 1960 of Adolf Eichmann, one of the Nazi architects of the Final Solution. The other involved Yosseleh Schumacher, the grandson of an ultra-Orthodox Brooklynite, who, in 1959, was prevented from kidnaping his son and enrolling him in a religious school.
In 1962, Harel learned that the Germans were assisting the Egyptians in developing missile technology. According to Reuven Merhav, former long-time member of the intelligence community, the technology was far inferior to Israel's and not a threat to her security; nevertheless, Harel believed it necessary to intimidate Germany. This angered Ben-Gurion.
As a result of irreconcilable differences with the Prime Minister, Harel resigned from the Mossad in 1963.
After his career in intelligence, Harel was primarily a writer. His best known book, The House on Garibaldi Street (1975), recounts the capture of Eichmann.
He died in Israel on February 19, 2003.