The 1998–99 Liga Bet season saw Hapoel Hurfeish (champions of the North A division), Maccabi Hadera (champions of the North B division), Hapoel Kiryat Ono (champions of the South A division) and A.S. Ramat Eliyahu (champions of the South B division) win the title. The four clubs were placed in Liga Alef, which became the fourth tier upon the creation of the Israeli Premier League. The rest of the clubs remained in Liga Bet, which became the fifth tier of the Israeli football league system.