Janet Hughes, the driving force behind Defra's Future Farming and Countryside Programme (FFCP), will step down next month after five years at the helm.
As part of the role, Ms Hughes was instrumental in helping to shape agricultural policy during a period of significant change for the industry.
She is set to take up the position of Director General for Civil Service Efficiency and Reform at the Cabinet Office in June.
"I’m massively grateful to everyone I’ve had the pleasure of working with over the last five years and hugely proud of the progress we’ve made together," she said on X.
The National Sheep Association (NSA) called her time as Programme Director at the FFCP as "transformative".
NSA chief executive Phil Stocker said: “Janet was the architect for several farming programmes during a huge state of flux for the industry and in many ways was the engineer of all the codesign work that took place in recent years.
“Her level of engagement will perhaps be her defining attribute. She ensured she was visiting farms and her team got out and about to learn about what was needed on the ground."
"She attended every one of NSA’s SFI pilot meetings over a period of two years, such was her interest and commitment in the job and her desire to get things right."
Mr Stocker added: “We wish her best luck in her new role, which sounds like a challenge but one she has the skills to meet.
"The fresh thinking Janet brings will be exactly what the civil service needs if it is to reform and increase efficiency in a very challenging environment.”
Defra will be opening applications for Programme Director of the FFCP shortly.