The 1999–2000 Liga Bet season saw 153 clubs competing in 11 regional divisions for promotion to Liga Bet.
Beitar Safed, Hapoel Maghar, Hapoel Bnei Manda, Hapoel Yafa, Maccabi Tzur Shalom, Hapoel Baqa al-Gharbiyye, Shimshon Bnei Tayibe, Maccabi Yehud, Beitar Holon, Hapoel Sde Uzziah/Be'er Tuvia and Hapoel Rahat won their regional divisions and promoted to Liga Bet.
Second placed clubs, Hapoel Ramot Menashe Megiddo, Hapoel Aliyah Kfar Saba, Maccabi Holon, Beitar Kiryat Gat and Moadon Tzeirei Rahat were also promoted, after several vacancies were created in Liga Bet.[1]
Beitar Kiryat Yam withdrew.
Maccabi Musmus withdrew.
Hapoel Jisr az-Zarqa, Maccabi Amidar Netanya and Maccabi Kfar Yona withdrew.
Hapoel Neve Golan withdrew.
Beitar Bat Yam and Maccabi Dynamo Holon withdrew.
Beitar Beit Shemesh and Hapoel Gedera withdrew.
Hapoel Bnei Laqiya withdrew.