Yagur was founded in 1922 by a settlement group called Ahva. Its name was taken from an Arab village called "Yajur" nearby. There is a site with a similar name (Jagur) mentioned in the Book of Joshua 15:21, though it was located in territory belonging to the Tribe of Judah, far to the south. At first, the members worked drying up the swamps surrounding the Kishon River and preparing the land for permanent settlement. They then established the various agricultural divisions, and the kibbutz began to grow. The economy is now based on diversified agriculture and industry.
During the Mandate era, Yagur was an important center for the Haganah. During Operation Agatha on 29 June 1946, the British army conducted a major raid on the kibbutz and located a major arms depot hidden there after receiving a tip from informants. The weapons were confiscated, and many members of the kibbutz were arrested
