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Founded in 1946, the club dwelt in the lower leagues until they won Liga Bet North A in the 1962–63 season and promoted for the first time to Liga Alef, the second division by then. In 1973–74, they won Liga Alef North division. However, the Israel Football Association decided that season on promotion play-off, involving the top 2 clubs in each Liga Alef division, and the bottom two clubs in Liga Leumit. after finishing in 5th position (out of 6), they were not promoted.

After second-place finish in the 1974–75 season, Hapoel won Liga Alef North division in the 1975–76 and were promoted to the top division for the first time. After finishing 11th (out of 16) in their first season, they won only two matches the next season, and were relegated to Liga Artzit, which was the new second division at the time. This proved to be their last appearance in the top division for the next 31 years.

In 1982–83 the club had dropped into Liga Alef, the third tier at the time. They promoted back to Liga Artzit at the end of the 1984–85 season, after winning the Promotion play-offs against Lazarus Holon, and remained there seasons at the second tier, until the 1987–88 season, where they finished bottom, and relegated to Liga Alef for the second time.

In 1998–99 they were promoted to Liga Artzit (the new third tier, due to the creation of the Israeli Premier League that summer). However, in 2003–04, the club finished as runners-up, and were promoted back to Liga Leumit. In 2005–06, the club won their first ever piece of silverware, picking up the second division's Toto Cup after beating Hapoel Be'er Sheva 5–3 on penalties after a 0–0 draw. In 2008–09, the club finished as runners-up, and promoted to the Premier League.

In the 2010–11 season, the club achieved its best placing to date, when they finished eighth in the Israeli Premier League.

On 3 June 2013, an agreement was signed between Hapoel Acre association and the municipality of Acre, and as a result, a new association was appointed by the municipality.

In the 2012–13 and 2014–15 seasons, the club finished at the bottom of the league at the end of the regular season. However, they avoided relegation in both occasions, following a strong finish of the bottom play-offs. In the 2015–16 season, the club finished second bottom and relegated to Liga Leumit, after seven successive seasons in the top division.