The club was established in 1928. In 1951–52 they won the South Division of Liga Bet to win promotion to Liga Alef (then the top division). Three years later they finished third from bottom and had to take part in promotion/relegation play-offs with the two top clubs from the second tier. They were unbeatnd during the play-offs and retained their place in Liga Leumit (which had replaced Liga Alef as the top division). However, in 1955–56, they finished bottom and were relegated.
Hapoel made an immediate return to Liga Leumit. They finished bottom in 1957–58, but avoided the drop as no clubs were relegated. However, they finished bottom again the following season and were relegated. The club returned to Liga Leumit in 1968. In 1975 they reached the State Cup final for the first time, beating Beitar Jerusalem 1-0. After several mid-table finishes, they were relegated at the end of the 1976–77 season. They made an immediate return to the top division, finishing third in Liga Artzit (the new second tier). In 1980 they reached the State Cup final again, beating Maccabi Ramat Amidar 4–1.
In 1980–81 they narrowly avoided relegation, finishing two points and one place above the relegation zone. The following season the club won the title for the first (and only) time under the management of Dror Kashtan. However, they finished bottom the season after, and returned to Liga Artzit.
They finished as runners-up to Hapoel Haifa in 1983–84 to make another immediate return to Liga Leumit. In 1990 the club reached the State Cup final for a third time, beating Shimshon Tel Aviv 1–0 after extra time. The following season they were relegated again after finishing bottom of the table. In 1992, under the management of Avram Marchinsky, the club signed its first American player, Michael Winograd, out of Lafayette College. The club returned to the top division the following season.
For the 2010–11 season, a new owner, Harel Raihman, came on after almost 15 years of Eli Tabib's era. At the end of the regular season, the club finished on top of the league, with an advantage of thirteen points over the third place. However, in the Top playoff, where all the points obtained during the regular season were halved (and rounded up), the club failed to record a win, and finished the league in the third place, behind Ironi Nir Ramat HaSharon and Hapoel Rishon LeZion which were promoted. As the third placed club, Kfar Saba went to play in the Promotion play-off against the 14th-placed club in the Israeli Premier League, Hapoel Petah Tikva, and lost both games, 1-4 and 0-1. Thus, the club remained in Liga Leumit.
In the 2012–13 season the club have entered administration, and as a result, were deducted nine points. The club finished bottom and relegated to Liga Alef, the third tier of Israeli football. With a new owner, Stav Shaham, together with former club captain, Eli Yani, and the supporters trust, "The Green Heart", the club recovered in the following season, and made an immediate return to Liga Leumit, after finishing on top of Liga Alef North division. In the following season, the club made their second successive promotion, following runners-up finish in Liga Leumit. Thus, the club returned to the Israeli Premier League after seven years.