Kaepernick was the driving force behind the controversial “taking the knee” movement. The protest act saw NFL American Football players kneel down during the US national anthem, which is played at the start of all NFL games. The movement was to raise awareness of police brutality towards the African-American community in the US.
The Kaepernick mural was created by artist Fabian Williams, who posted a video of the destroyed site on social media on Friday – two days before Atalanta hosts Super Bowl 53.
Taking to Instagram after the incident, the artist wrote: “Think about that.
“The way they kick off the celebration if the NFL most watched event, they tear down the building with their most talked about professional athlete without a job, Colin Kaepernick.
“What did he kneel for? Inequality. Human rights.
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“That’s the symbol that they just demolished during their celebration.
“Timing is important and it’s a message.”
Mr Williams is best known for his anti-racism work depicting the allegedly state-sanctioned violence perpetrated against black men.
The artist created the mural of Kaepernick as a tribute to the fight against racial injustice in the US.
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Kaepernick’s “taking the knee” protest movement attracted controversy in the states and was banned by the NFL.
The 31-year-old quarterback played for San Francisco 49ers before leaving the club in March 2017.
Mr Williams said the owner of the building on which the mural was painted had liked the work, but that “the city was complaining to him about it”.
The building lies about a mile from Mercedes-Benz Stadium, which will host Sunday’s extravaganza, and Mr Williams had planned to spruce up the mural before then, the Atlanta Journal-Constitution said.
The artist noted the destruction of the site so close to the game was “odd”.
He said: “I figured at some point they would tear the building down, but it has been sitting up this whole time.
“The fact that the Super Bowl happens here and the weekend when the festivities are gearing up, the building gets demolished is very odd.”