The season began on 1 November 1998 and ended on 9 April 1999.
PSIS won the title after beating the defending champions, Persebaya 1–0 in the final.
Persiraja won on away goals and retained their spot in the Premier Division, Persita were relegated.
Gelora Dewata won 7–5 on aggregate and retained their spot in the Premier Division, Persikabo were relegated.
The following is a list of the top scorers from the 1998-99 season.