The 2006–07 Liga Bet season saw Beitar Ihud Mashhad (champions of the North A division), Ironi Sayid Umm al-Fahm (champions of the North B division), Maccabi Ironi Kfar Yona (champions of the South A division) and Maccabi Ironi Netivot (champions of the South B division) winning the title and promotion to Liga Alef.
The runners-up in each division entered a promotion/relegation play-offs with the clubs ranked 12th in Liga Alef. In the north section, Ironi Tiberias (from North B division) won the play-offs and was promoted. In the south section, Hapoel Tzafririm Holon from Liga Alef won over both runners-up and remained in Liga Alef. However, since Hapoel Maxim Lod folded over the summer, South A division runner-up, Beitar Kfar Saba was also promoted.
At the bottom, Hapoel Kisra, Hapoel Deir Hanna (from North A division), Hapoel Kiryat Ono, Hapoel Ihud Bnei Jaffa (from South A division), Maccabi Kiryat Ekron and Hapoel Bnei Lakhish (from South B division) were all automatically relegated to Liga Gimel. In North B division, Hapoel Tel Hanan and Maccabi Daliyat al-Karmel were both had their activity suspended during the season and were demoted to Liga Gimel.
1. Four points deducted.
During the season, Hapoel Tel Hanan and Maccabi Daliyat al-Karmel failed to show to fixtures and were punished with suspension of activity, their record was annulled and the clubs were demoted to Liga Gimel.