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The club was founded in 2008 after Hapoel Gilboa (which had previously been merged with Hapoel Afula, which regained its independence) receive the top-division license in the Israeli Basketball Premier League of Hapoel Galil Elyon.

Initially it was believed to be a merger agreement, as they originally planned to play 70% of the club's home domestic league games at Gan Ner Sports Hall in Gan Ner (a village of 2,700 people near Mount Gilboa, in the Galilee in northern Israel) and 30% of their home domestic league games in Hapoel Galil Elyon's arena in Kfar Blum. But the agreement never came to fruition as Hapoel Galil Elyon rejected the merger, and all of the club's home domestic league games were played in Gan Ner, essentially making them a new team. Galil Elyon was re-established in 2009, as a lower-division team.

In May 2010, Hapoel Gilboa Galil won the Israeli Championship, after defeating defending champions Maccabi Tel Aviv by a score of 90–77 in the finals of the playoffs.

In the summer of 2018, the club had financial difficulties, and a large part of it was purchased by fans.