The 81-foot (25-metre) flagpole was put up without planning permission at the billionaire's Trump International Golf Links in Scotland, the country where his mother was born.
The giant pole, used to fly a saltire (Scotland's flag), is situated near the clubhouse of the Aberdeenshire course.
When the relevant approvals were sought retrospectively, a committee at Aberdeenshire Council refused in April to grant full permission for the flagpole "on the grounds of the visual impact... due to its scale".
But Trump, elected last week to be the next president of the United States in a stunning victory, has now been allowed to keep the structure following an appeal to Scottish ministers.
A spokeswoman for Trump International Golf Links in Scotland said: "We are pleased that our appeal to fly our national flag was successful and that common sense has prevailed."
Trump's golf resort in Balmedie, a village on the shores of the North Sea, has been deeply controversial locally.
Members of the community said he broke promises on creating jobs and rode roughshod over concerns about construction.
The tycoon has two golf courses in Scotland.