The 1998–99 Liga Alef season was held between 11 September 1998 and 29 May 1999. It was the last season (until 2009–10) in which Liga Alef was the third tier of Israeli football, as the creation of the Israeli Premier League in the summer of 1999 meant that it became the fourth tier. Due to the restructuring, two clubs were due to be promoted from each division; Hapoel Ra'anana and Hapoel Nazareth Illit from the north and Hapoel Dimona and Hapoel Ramat Gan from the south.