Neil McGovern, a Debian developer for 12 years and leader of the project from 2015-16, will start in his new role on 15 February.
He has been on the boards of numerous projects in the past, including Software in the Public Interest and the Open Rights Group.
McGovern, who is based in the UK, has worked with the open-source company Collabora as engineering manager.
GNOME Foundation president Nuritzi Sanchez said: "The GNOME Foundation board of directors is thrilled that Neil will be joining in the capacity of executive director. Neil was a very strong candidate, and we have high hopes for what he will enable the GNOME community to achieve."
The chief executive of Collabora, Philippe Kalaf, said: "Through the past five years, Neil has helped us grow, develop, and maintain our strong engineering team. His technical knowledge and dedication to Open Source will be a great asset to the GNOME Foundation."
It is three years since GNOME Foundation had an executive director. Karen Sandler, who was in the role, quit to take up a role with the Software Freedom Conservancy.
Reacting to the news, Sandler said: "As former executive director of the GNOME Foundation, it’s clear to me that Neil is a fantastic choice for the position. His insights into both the community and corporate sides of GNOME are impressive. I know GNOME will thrive under his leadership."
The current Debian leader, Mehdi Dogguy, said he hoped that McGovern would help to forge closer relations between the two projects.
"Neil’s commitment to free and open source software over the years make him a great asset to the community. I believe his new role as executive director of the GNOME Foundation will help to make a stronger link between GNOME and the Debian project," Dogguy said.