The powered parachute was organised by Greenpeace and appeared over the luxury Turnberry Hotel at around 9.45pm on Friday, with a banner reading “Trump Well Below Par” unfurled on the roof.
Although Greenpeace insisted it had informed police of the plans in advance, the protester was said to have breached a no-fly zone and committed a criminal offence.
Police Scotland said in a statement: “A 55-year-old man has been arrested and has now been charged in connection with an incident when a powered parachute was flown in the vicinity of the Turnberry Hotel around 9.45pm on Friday 13 July 2018.”
The man will appear at Ayr Sheriff Court on Monday.
1:27 Video: Trump's visit marked by protests
More protests followed when Mr Trump took to the course on Saturday, with those keen to denounce the president taking to a nearby beach and hills overlooking the greens to chant: “No Trump, no KKK, no racist USA.”
Mr Trump appeared non-fussed as he drove his buggy from hole to hole sporting a USA baseball cap, as other demonstrations took place in Glasgow and outside the Scottish parliament building in Edinburgh.
The giant baby blimp depicting Mr Trump as a snarling, orange, nappy-wearing infant also made an appearance in Edinburgh, after being granted approval to fly by mayor Sadiq Khan.
Image: A number of protests took place in Scotland to mark the US president's arrival
Appearing on the ‘s Andrew Marr Show on Sunday, Mr Khan – who has been embroiled in several spats with the president since the two were elected – defended his decision.
He said it was “not my job as mayor to censor the views of Londoners” and pointed out how the “extreme far-right” and pro-Trump supporters were also allowed to protest in the capital on Saturday.
When asked if the president had repeatedly criticised him because he was Muslim, Mr Khan said it was not for him to answer and added that he did not think Mr Trump was racist.
0:59 Video: Moment the Trump baby blimp takes off
But – citing his promotion of far-right group Britain First and his language about immigrants – he said: “You understand why people draw the conclusion he‘s racist.”
Mr Trump‘s former chief strategist Steve Bannon told LBC that suggestions of racism from critics was a sign that “you know you are winning”.
He said the “historic lows” of black and Hispanic unemployment in the US was evidence that Mr Trump was an “anti-racist, citing his immigration and “economic nationalism” policies.
Before the protests in Scotland, Mr Trump had marked his arrival on Twitter, posting: “I have arrived in Scotland and will be at Trump Turnberry for two days of meetings, calls and hopefully, some golf, my primary form of exercise!”
It was one of a number of memorable quotes from the president during his UK trip.
He followed it up with another tweet in which he reaffirmed his plans to meet with Vladimir Putin in Helsinki on Monday, in which .
Image: Mr Trump has been enjoying some golf while in Scotland
He has said he expects talks with the Russian leader to produce “nothing bad” and “maybe some good”, and is due to jet off to Finland from Glasgow Prestwick Airport with wife Melania later on Sunday – after a bit more golf.
Mr Trump will depart the UK having left Theresa May with the job of clearing up a number of controversial comments he made during his visit, including his advice for how to negotiate Brexit.
The prime minister has , having already faced suggestions from him that her strategy would “kill” hopes of a US-UK trade deal.
Although Mr Trump later following talks with Mrs May on Friday, the US president confirmed Mrs May had ignored his “suggestion” on how to deal with Brexit negotiations as “maybe too brutal”.