The 1999-00 Allied Dunbar Premiership Two was the thirteenth full season of rugby union within the second tier of the English league system, currently known as the RFU Championship.

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

New teams to the division included West Hartlepool who had been relegated from the Allied Dunbar Premiership 1998–99 while Henley Hawks and Manchester had been promoted from National League 1.

[2] Rotherham, the champions, were promoted to the Allied Dunbar Premiership for season 2000–01 after beating the 12th placed team from that division, (Bedford), in a two legged play–off.

There was only one promotion place available and the runners–up Leeds Tykes remained in Premiership Two for the following season.