The 1999–2000 Liga Bet season saw 153 clubs competing in 11 regional divisions for promotion 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.
Hapoel Jisr az-Zarqa, Maccabi Amidar Netanya and Maccabi Kfar Yona withdrew.
Beitar Bat Yam and Maccabi Dynamo Holon withdrew.
Beitar Beit Shemesh and Hapoel Gedera withdrew.