The 1998-99 Allied Dunbar Premiership Two was the twelfth full season of rugby union within the second tier of the English league system, currently known as the RFU Championship.

The league was expanded from twelve teams to fourteen and new teams to the division included Bristol who had been relegated from the Allied Dunbar Premiership 1997–98 while London Welsh, Rugby Lions, Leeds Tykes and Worcester were promoted from National League 1.

Allied Dunbar sponsored the top two divisions of the English rugby union leagues for the second season in a row.

Bristol, the champions, were promoted to the Allied Dunbar Premiership for season 1999–00.

The runners–up Rotherham lost to the thirteenth placed team in the Premiership (Bedford) in a two legged play–off and did not gain promotion.