Hill said he and his girlfriend were at about 1,200 feet high when the bullet came through their side window and up into the roof. They were over the Talleyrand area, just north of the Mathews Bridge.
Hill said he thinks he was hit by a stray bullet and the couple's plane wasn't targeted.
"Unless it was a high powered rifle I don't think they'd be able to do it," said Hill.
The pilot's head is healing, and he's back in the sky. But he's left irritated that this happened and no one's been arrested.
"(I have) just anger more than anything," said Hill. "We're up here, it's a beautiful place at night. It's a nice way to bring in new years above the city, and it got ruined because of somebody not thinking, shooting the gun up in the air."
And now he's asking for the public's help in solving this case.
"I think they might be able to find the person, the shooter," Hill told Channel 4. "It's a small, nine-block neighborhood. And I've got the bullet. So if anybody would come forward it'd be a great deal of help."
Could have ended in tragedy
Attorney Ed Booth has been a pilot for 35 years. He said besides hitting the people inside, the bullet could have ruptured a fuel tank and or the engine.
"It could have easily caused the aircraft to explode," said Booth, who is not related to the case. "Here in the cockpit you're sitting on top of 50 gallons of highly flammable, explosive aviation gasoline.
And if the plane crashed, there were thousands in the danger zone, out and about, getting ready to watch the fireworks show on the riverbanks.
Melissa Bujeda with the Jacksonville Sheriff's Office said no one's been arrested for what happened, and whether the shot at the plane was intentional or not, it was a crime.
"It's called discharging a firearm in public and it's illegal," Bujeda said.
She said for whatever reason some people like to shoot their guns in the air on New Year's as part of the celebrations.
"We get hundreds of calls between New Year's Eve and New Year's Day," said Bujeda.
One of those calls was from the family of an 8-year-old boy, whom police said apparently was hit by a stray bullet just minutes before the stroke of midnight on the Southbank of the St. Johns River. No one's been arrested in that case either, but he's recovering, knowing it could have been much worse.
Between 9 p.m. New Year's Eve and 3 a.m. New Year's Day, the Jacksonville Sheriff's Office received 154 calls about shots fired.
A handful of those calls came from Talleyrand -- the area Hill was flying over.
"Identifying the shooter is the real problem," said Booth, a former Jacksonville prosecutor. "In this case it will be very difficult to track this person down without some assistance from the people in the neighborhood who certainly witnessed this."
Booth said if police do track down the shooter, he or she could face serious consequences.