The banner read Trump Well Below Par and was revealed shortly after the US president arrived at the Ayrshire hotel on Friday.
Police Scotland said in a statement: “Police Scotland can confirm that 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.”
He is expected to appear at Ayr Sheriff Court on Monday and a report will be submitted to the Procurator Fiscal.
The force earlier said the incident was being treated as a breach of the air exclusion zone that was in place.
The president and his wife Melania are staying at the Turnberry resort this weekend during a private leg of their visit to the UK, after Trump had meetings with Theresa May and the Queen.
The US played golf at his Turnberry resort on Sunday morning as police announced they had arrested a man in connection with an aerial protest at the hotel.