The president said on Twitter that Mr McAleenan has done an outstanding job and border crossings are down.
"Kevin McAleenan has done an outstanding job as Acting Secretary of Homeland Security".
In an interview with the Washington Post, published on October 1, he complained that he does not control "the tone, the message, the public face and approach of the department in an increasingly polarized time", describing that as "uncomfortable" situation for the acting department chief.
The president added that the new acting homeland security secretary would be announced next week and said he had "Many wonderful candidates" to fill the position.
The departure continues a purge of leadership at the Department of Homeland Security at Trump's behest and raises more uncertainty over management at the massive agency created after the September 11 terrorist attacks.
I will be announcing the new Acting Secretary next week.
McAleenan was successful in sharply curbing border crossings, which had bedeviled his predecessors and had led to the departure of Kirstjen Nielsen, who had the job before McAleenan.
Trump, who has made cracking down on legal and illegal immigration a signature issue of his presidency and 2020 re-election effort, said he and McAleenan had "worked well together with Border Crossings being way down".
U.S. Customs and Border Protection said this week that arrests at the U.S. -Mexico border fell in September for the fourth month in the row.
He was well-liked among Republican and Democratic administrations.
But he quickly drew scrutiny from hard-liners close to Trump for his ties to the Obama administration, where he was deputy commissioner of the agency.