A total of 11 teams contested the league.

The Townsville Suns were renamed the Townsville Crocodiles The 1998–99 regular season took place over 23 rounds between 9 October 1998 and 14 March 1999.

Updated to match(es) played on 14 March 1999.

Source: NBL.com.au The NBL tie-breaker system as outlined in the NBL Rules and Regulations states that in the case of an identical win–loss record, the results in games played between the teams will determine order of seeding.

3Townsville Crocodiles won Head-to-Head (2-1).