Health minister since 2003, Lord Warner was previously special adviser to Jack Straw, when he was home secretary, and then chairman of the Youth Justice Board for England and Wales.
'Health reforms have made a huge difference and you have made remarkable steps forward during your time in the department.'
Lord Warner said: 'It is entirely my decision and I will continue to strongly support the NHS reform agenda in the House of Lords and elsewhere.'
NHS Confederation chief executive Gill Morgan said Lord Warner had been a 'steady hand at the tiller' on the NHS.
'There is clear evidence that the NHS is turning a corner. There are still challenges ahead but with the new framework of pay contracts and an enabling IT system we believe that when people look back they will see Lord Warner as one of the major architects of a 21st Century NHS.'