The tycoon plans to replace the current temporary structure with a new £5 million granite building overlooking his Menie Estate championship links.
The American businessman had vowed to put all further development at the site on hold over a proposed windfarm in Aberdeen Bay.
But he also said it would be "disrespectful" not to give the course the building it deserves.
The clubhouse could be the final piece of the jigsaw he needs to lure the Scottish Open or the Open Championship.
Mr Trump said: "The course has turned out to be a phenomenal success and has received some of the greatest reviews ever given to a course. I felt it was only fair that I build a beautiful new clubhouse. It would be disrespectful not to have done so.
"When completed, our clubhouse at Trump International Golf Links, Scotland will be a true classic."
Andy McNair, director of architects Covell Matthews, said: "The proposed clubhouse draws precedent from the style, details and materials to create a building that is in keeping with the aesthetic of Menie Estate."