The 1999–2000 Liga Leumit season was the first in which Liga Leumit was Israeli football's second tier, following the establishment of the Israeli Premier League in the summer of 1999. Due to the ongoing restructuring, the league had only 10 clubs (expanded to 12 the next season as three clubs were relegated from the Premier League and only one promoted). Tzafririm Holon won the title and were promoted, whilst Hapoel Ashkelon finished bottom and were relegated to Liga Artzit. Holon's Danny Nir'on was the league's top scorer with 23 goals.