Lute has more than 30 years of military and government experience and has previously served as a top official at the United Nations, where she worked on peacekeeping operations.
Her imminent departure comes on the heels of another top DHS official announcing plans to step down. Mark Weatherford, deputy under secretary for cybersecurity at the department, said last month that he will be leaving the DHS to serve as a principal for The Chertoff Group.
The executive order affirmed the Obama administration's commitment to having the department lead the federal government's cybersecurity efforts.
Napolitano thanked Lute for her service in a statement and noted that one of Lute's top accomplishments at the department included spearheading its efforts to enhance the federal government's cybersecurity and protect the country's critical infrastructure from cyberattacks.
"She was instrumental in the department's effort to implement recommendations by the Homeland Security Advisory Council Task Force on CyberSkills, to ensure that DHS expands the pipeline of men and women with advanced cybersecurity skills, and enables us to become a top competitor for cybersecurity talent," Napolitano said.
"Because of her service, our nation is safer, more secure and more resilient. I wish her all the best in her next endeavors," the secretary added.
A spokesman for the DHS did not respond to a request for comment about Lute's departure.