The museum called it a "preparatory measure".
"Today's activity is rather of a symbolic character ahead of the elections in the United States," the museum's marketing manager Orkide Yalcindag told Reuters.
"We here at Madame Tussauds Berlin removed Donald Trump's waxwork as a preparatory measure."
The museum includes wax figures of several former US presidents, regardless of what happened to them in subsequent elections.
Trump has been trailing behind Democratic candidate Joe Biden in most polls but seems to be gaining ground in some key states.