"Congratulations Kevin, on a job well done. I will be announcing the new Acting Secretary next week. Many wonderful candidates."
McAleenan became the Acting chief of Department of Homeland Security (DHS) in April, after former DHS secretary Kirstjen Nielsen resigned.
Vice President Mike Pence also in a tweet said "Thank you Kevin McAleenan for your dedication and service to our country! You have done great work securing our border and we are thankful for your continued support of President and our entire administration."
McAleenan, who oversaw an aggressive campaign to curb illegal immigrants from entering the US from its southern border, voiced his frustrations to the press last week about the job.
"What I don't have control over is the tone, the message, the public face and approach of the department in an increasingly polarized time," he had told the Washington Post.
Adding to his frustration was the White House's reluctance to nominate him as the secretary of the department, which undermined his authority.
Anti-immigration is a focus of Trump's policies, which has often put the DHS under the scrutiny of the US media as it carried out raids and stepped up arrest of illegal immigrants.
McAleenan was the fourth official to lead the DHS under Trump and the second Acting secretary.
John Kelly and Nielsen was the first and second Secretary of Homeland Security respectively.