Christine Connelly, chief information officer for health, has resigned ahead of a shakeup of the department.
In a statement she said: “The Department of Health faces a major reorganisation of its top structures that will result in fewer Director General posts. I have been reflecting on whether I would wish to go for one of those roles and decided that I will not."
She said she had decided that now was the right time to "step back and think about what I might do next".
The National Programme for IT - the £12.7bn project to improve technology use within the NHS - is facing major changes as part of coalition cutbacks.
Connelly was paid just over £200,000 in 2009 to 2010.
Connelly's interim replacement is Katie Davis. She previously revelled in the title of executive director of operational excellence in the Efficiency and Reform Group. Prior to that she worked on ID cards at the Home Office. ®