Jacob Hall was shot by a teenage gunman who killed his own father before the rampage in Townville, South Carolina.
Another child and a teacher were also wounded in the attack.
Jacob's family asked mourners to dress as the superheroes Jacob loved and he is being laid to rest dressed as Batman.
His blue casket was decorated with Teenage Mutant Ninja Turtle stickers and figurines of Ninja turtles and Captain America.
Six-year-old Lily Gunby, who attended the funeral dressed in a pink and black superman shirt, said Jacob "was really sweet" and "knew a lot about Jesus".
Her uncle, Derek Gunby, said Jacob was "the cutest thing ever" at the church's Bible school.
Police in South Carolina have been showing support by dressing as superheroes such as Captain America, the Punisher and Spider-Man.
Townville Elementary teachers also attended the funeral, with some wearing handmade blue capes and Ninja Turtle masks.
Jacob had told his family he wanted to be a preacher one day, and the Reverand Tim Marcengill told a crowd that packed the pews at the family's Oakdale Baptist Church: "He's preaching today."
He also said Jacob was "Townville's very own superhero".
Jacob died several days after a gunshot wound pierced an artery in his leg.
The 14-year-old gunman was subdued by a volunteer firefighter before he could enter the school and harm more students.
The attack happened just as students were being let outside for recess break on 29 September.
People dressed in superhero costumes have attended the funeral of a six-year-old boy who was shot to death at his primary school last week.