Mayor Robert Smith said Hill made a "heroic stand in the face of adversity" when he tweeted in June that he would not represent Mississippi as long as the state's flag, which featured the Confederate battle emblem, remained unchanged.
A week after Hill's tweet, following a trip by Mississippi State coach Mike Leach, Ole Miss coach Lane Kiffin and others to lobby at the state capitol, lawmakers voted to change the flag to one that won't feature the symbol of the Confederacy.
"He received a lot of backlash, a lot of negative comments," Smith said. "The city of Columbus is proud of the stand Kylin has taken considering the flag."
Hill said it felt "unreal" to be given the keys to the city.
"We have all these big-time athletes who have a voice but won't speak on it," he said. "I said, why not me? That's the thing -- you can't be scared to speak up. Being scared to speak up, the situation will never get handled."
Hill, 22, an All-SEC selection who bypassed the NFL draft to return for his senior season, went to Columbus High School where he was considered a top-10 prospect in the state and chose to go to college at nearby Mississippi State despite offers from several FBS schools, including Ole Miss and Tennessee.
Mississippi State athletic director John Cohen joined Hill in Columbus where he was given the ceremonial key to the city by Smith and district attorney Scott Colom.
"Kylin is a courageous young man who did a bold and brave thing," Cohen said. "He shared an emboldened belief held by many Mississippians that a paradigm-shifting change needed to be made. It was time for a new flag."
Cohen added: "There's much more to Kylin Hill than just a tweet. Kylin's an exceptional athlete. Kylin is an exceptional student. Kylin continues to make a positive impact on his community."
Last season, Hill rushed for 10 touchdowns and 1,350 yards, which ranked third in the SEC. He also caught 18 passes for 180 yards a touchdown.