New Hope chairman Robert Millner said Stephan had been at the company for 11 years, firstly as chief financial officer, and then in February 2014, taking on the position of CEO and subsequently, managing director.
"Shane has led the company through challenging times associated with the process of seeking the approvals for the New Acland Stage 3 extension," Millner said.
"He has also led the company through a period of growth, with the acquisition of the company's 80% interest in the Bengalla mine."
The board has appointed Korn Ferry to assist with the process of selecting an appropriate successor from a pool of both internal and external candidates.
Millner said sales tonnages had more than doubled during Stephan's time as CEO, while the company had maintained its record of tight cost control.
Stephan said: "Having started my career in the Ipswich coal fields as a cadet mine manager 39 years ago, I have had the privilege of undertaking many roles in my career, culminating in my current role as CEO of New Hope.
"The highlight of my term as CEO of New Hope has been the completion of the sequence of acquisitions leading to the company holding an 80% interest in and management of the world class Bengalla mine."