The 203-year-old church has played an important role in the history of South Carolina, including the slavery era, the civil rights movement, and Black Lives Matter. The church was founded in 1816 and it is the oldest African Methodist Episcopal Church in the South, often referred to as "Mother Emanuel". It is the oldest historically black congregation south of Baltimore. When one of the church's co-founders, Denmark Vesey, was suspected of planning a slave rebellion in Charleston in 1822, 35 people, including Vesey, were hanged and the church was burned down. Charleston citizens accepted the claim that a slave rebellion was to begin at the stroke of midnight on June 16, 1822, and to erupt the following day; the shooting in 2015 occurred on the 193rd anniversary of the thwarted uprising. The rebuilt church was formally shuttered with other all-black congregations by the city in 1834, meeting in secret until 1865 when it was formally reorganized, acquired the name Emanuel ("God with us"), and rebuilt upon a design by Denmark Vesey's son. That structure was badly damaged in the 1886 Charleston earthquake. The current building dates from 1891.
The church's senior pastor, the Rev. Clementa C. Pinckney, had held rallies after the shooting of Walter Scott by a white police officer two months earlier, in nearby North Charleston, and as a state senator, Pinckney pushed for legislation requiring police to wear body cameras. Several observers noted a similarity between the massacre at Emanuel AME and the 16th Street Baptist Church bombing of a politically active African-American church in Birmingham, Alabama, where the Ku Klux Klan (KKK) killed four black girls and injured fourteen others, an attack that galvanized the civil rights movement.
A number of scholars, journalists, activists and politicians have emphasized the need to understand the attack in the broader context of racism in the United States, rather than seeing it as an isolated event of racially motivated violence. In 1996, Congress passed the Church Arson Prevention Act, making it a federal crime to damage religious property because of its "racial or ethnic character", in response to a spate of 154 suspicious church burnings since 1991. More recent arson attacks against black churches included a black church in Massachusetts that was burned down the day after the first inauguration of Barack Obama in 2009.