The competition was also integrated into the league fixtures with the first round of games between teams (home and away) counting towards the Challenge Cup table and the league table.
In the 1998–99 season, sixteen teams in total were split into four groups (two ISL and two BNL) playing each team in their group once at home and once away.
The first round was the first home and away meeting of each team in the league with the points counting towards both the Challenge Cup table and the league table.
Group A consisted of Bracknell, London, Manchester and Sheffield while Group B consisted of Ayr, Cardiff, Newcastle and Nottingham.
The top two teams from each playoff group qualified for the finals weekend.