Ryan Wesley Routh faces charges of possessing a firearm despite being a convicted felon and possessing a firearm with an obliterated serial number.
He appeared briefly in federal court in West Palm Beach on Monday (close to midnight on Tuesday AEST).
Additional and more serious charges are possible as the investigation continues and prosecutors seek an indictment.
The episode occurred on Sunday afternoon (early Monday AEST) when Secret Service agents stationed a few holes up from where Trump was playing noticed the muzzle of an AK-style rifle sticking through the shrubbery that lines the course, roughly 400 metres away.
An agent fired and Routh dropped the rifle and fled in an SUV, leaving the firearm behind along with two backpacks, a scope used for aiming and a GoPro camera, the authorities said.
Routh was later stopped by law enforcement in a neighbouring county.
