Hapoel Isfiya has played their entire history in the lower divisions of Israeli football.

Hapoel Isfiya were re-established after Maccabi Isfiya had folded at the end of the 2002–03 season, and upon its re-establishment, received the players from the defunct club and joined Liga Gimel, Samaria division.

In 2005, the club became known as Hapoel Ironi HaCarmel, named after the short-lived Carmel City, which was a merger of Isfiya and Daliyat al-Karmel.

However, after the merger was canceled in 2008, the club was renamed back to Hapoel Isfiya.

Hapoel Isfiya appeared in the 34th episode, "Football", of the Israeli TV series Hafuch, when Anat (played by Einat Weitzman),[6] became richer following an investment in the stock market, until she mistakenly bought Hapoel Isfiya.