McAleenan became interim head of the department in April after former Secretary Kirstjen Nielsen's departure. McAleenan, whom Trump never formally nominated to serve in the position, was the fourth person to head the department.
"Kevin McAleenan has done an outstanding job as Acting Secretary of Homeland Security. We have worked well together with Border Crossings being way down. Kevin now, after many years in Government, wants to spend more time with his family and go to the private sector," Trump tweeted.
Trump said he planned to announce a new acting secretary next week.
McAleenan said he and the president "have made tremendous progress mitigating the border security and humanitarian crisis we faced this year."
"I will work with the White House and DHS leadership teams on a smooth transition, and remains forever grateful to the men and women of the Department for their steadfast efforts to secure our country," he said.