The 2008–09 Liga Alef season was the last season of Liga Alef as the fourth tier of the Israeli football league system. Third tier, Liga Artzit, was scrapped, while the Premier League and Liga Leumit were expanded to 16 clubs each, making Liga Alef the third tier, as well as expanding the two regional divisions to 16 clubs.
The season saw Ahva Arraba (champions of the North Division) and Maccabi Be'er Sheva (champions of the South Division) winning the title and promotion to Liga Leumit.
At the bottom, the bottom clubs in each division, Maccabi Ironi Shlomi/Nahariya, Beitar Ihud Mashhad (from North division), Ironi Ramla and Hapoel Masos/Segev Shalom (from South division) were all automatically relegated to Liga Bet, whilst the two clubs which were ranked in 12th place in each division, Maccabi Kafr Qara and Hapoel Nahlat Yehuda entered a promotion/relegation play-offs, and both remained in Liga Alef after winning the play-offs.
At the end of the season no relegation play-offs were held. The two bottom clubs were relegated automatically, while the third from bottom club was safe from relegation.
The 12th-placed team, Maccabi Kafr Qara, faced the Liga Bet promotion playoff winner Hapoel Daliyat al-Karmel.