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A Hapoel Ra'anana was established in 1938. They were placed in the South Division of Liga Bet (then the second division) in 1951–52.

The modern club was established in 1972, and in the mid-1990s was playing in Liga Gimel, the lowest tier of Israeli football. In 1995 they started a remarkable period of success after they won their division of Liga Gimel and were promoted to Liga Bet. In 1997–98, they won Liga Bet South A division and were promoted to Liga Alef. In 1998–99 they won the North Division of Liga Alef to earn promotion to Liga Artzit. After finishing third in 1999–2000, they won the league the following season and were promoted to Liga Leumit.

In 2008–09, the club was promoted to the Israeli Premier League for the first time in their history. However, they had to play its home matches at Hapoel Kfar Saba's Levita Stadium, as its home ground, the Karnei Oren Memorial Field, did not meet Premier League requirements. In January 2010, the city council published plans for a 7,500-capacity new stadium in Lev HaPark neighborhood.

After a single season in the top division, in which the club finished at the second bottom place, Ra'anana were relegated to Liga Leumit.

After three seasons in Liga Leumit, in 2012–13, Ra'anana finished runners-up and were promoted again to the Israeli Premier League. In the 2015–16 season, the club achieved its best placing to date, when they finished sixth in the Israeli Premier League.

In the 2019–20 season, Hapoel Ra'anana were relegated after suffering a 1-0 defeat to Ironi Kiryat Shmona, after 7 seasons in the top flight.