The runners-up in each division entered a promotion/relegation play-offs with the clubs ranked 12th in Liga Alef.
However, Hapoel Deir Hanna (from North B division), Maccabi Daliyat al-Karmel (from North B division) and Hapoel Bnei Lakhish (from South B division), which finished in the relegation zone, were all reprieved from relegation, after several vacancies were created in Liga Bet for the 2006–07 season, mostly due to withdrawals and mergers of clubs.
During the season, Hapoel Ironi I'billin (after 13 matches) folded and its results were annulled.
The teams played each other in a round-robin tournament, with all matches held at a neutral venue, Kiryat Eliezer Stadium.
The teams played each other in a round-robin tournament, with all matches held at a neutral venue, Bat Yam Municipal Stadium.