Curt James Brockway, 39, was arrested at a county rodeo on Saturday, telling police he asked the boy to remove his hat out of respect before the playing of The Star-Spangled Banner.
The boy swore at Brockway, at which point the 39-year-old grabbed the child by the throat, "lifted him into the air and slammed the boy into the ground," according to recently released court documents.
Details about the condition of the boy were not originally released, but the new documents filed by the county's attorney Ellen Donohue say the boy was flown to a hospital in Washington state for a possible concussion and fractured skull.
The boy has since been released from hospital.
A witness, Taylor Hennick, was at the rodeo at the time of the alleged attack.
She told local media that she heard a "pop", then saw the boy on the ground with blood coming from his ears.
Ms Hennick said the alleged attacker told her the boy "was disrespecting the national anthem so he had every right to do that."
Ms Donohue wrote that an unnamed witness agreed with Brockway's version of events, but that they did not hear him asking the child to remove his hat.
Brockway made his first court appearance on Monday, where the prosecution recommended his bail be set at $100,000 (£82,000).
It is not the first time that conduct during the playing of the national anthem has been an issue in the US.
In 2016, NFL player Colin Kaepernick knelt on one knee during the playing of the anthem to protest against the treatment of minorities.
"I am not going to stand up to show pride in a flag for a country that oppresses black people and people of colour," he said at the time.
American's have a flag code for when the national anthem is playing.
All people should face the flag during the anthem. It states that those in the military who are in uniform should salute, while those who aren't may also do so.
Male members of the public should remove their hats, and all members of the public should put their right hand over their heart, the code says.
Kaepernick's action prompted more player to join in with the protests, but sparked a backlash from some NFL fans.
US President Donald Trump spoke at the time, calling for a boycott of the league.
"Wouldn't you love to see one of these NFL owners, when somebody disrespects our flag, to say, 'Get that son of a b**** off the field right now. Out! He's fired. He's fired!'" Mr Trump said at a rally.
There is, however, no indication that the boy who was attacked was protesting.