The president and his wife, First Lady Michelle, will be in Charleston, South Carolina, for the service of Revd Clementa Pinckney.
He was leading a Bible study at the black Emanuel AME church in the city last Wednesday night when a white gunman opened fire killing nine people.
A shooter, 21-year-old Dylann Roof, has been charged with nine counts of murder.
The other victims of the attack were Cynthia Hurd, 54, Revd Sharonda Coleman-Singleton, 45, Tywanza Sanders, 26, Ethel Lance, 70, Revd Depayne Middleton-Doctor, 49, Susie Jackson, 87, Revd Daniel Simmons Sr, 74 and Myra Thompson, 59.
Mr Obama will give the eulogy at TD Arena in the city, where thousands of people are expected at the service.
Speaking immediately after the shooting, the President confirmed he and his wife were friends with the pastor and his family.
"Michelle and I know several members of Emanuel AME Church. We knew their pastor, Revd Clementa Pinckney, who, along with eight others, gathered in prayer and fellowship and was murdered last night," he said.
He added: "To say our thoughts and prayers are with them and their families, and their community doesn't say enough to convey the heartache and the sadness and the anger that we feel."
Revd Pinckney's body has been lying in an open casket at St. John AME Church in Ridgeland before the funeral.
Mr Obama met the pastor, who was also a state senator, during the 2008 presidential campaign.
Yesterday hundreds of people gathered for the funeral services of Revd Sharonda Coleman-Singleton and Ethel Lance.
A choir and band performed Gospel music as mourners stood, clapped, nodded and swayed.
Ms Lance, 70, had an "infectious smile", Revd Norvel Goff said.
He added: "When sister Lance praised the Lord, you had to strap on your spiritual seat belt."
Bishop Robert Guglielmone, from the Roman Catholic Diocese in Charleston told Premier Charleston is coping well: "I see tremendous opportunity for healing and even stronger relationships within people.
"I certainly believe the tension will be decreased as time goes on.
"Their lives will not be in vain."
He added that Christians can pray "that there continue to be a sense of calm and that we continue to strengthen the bonds that unite us."
Bishop Mark Lawrence, from the Diocese of South Carolina, also commented.
He told Premier's News Hour that the city will not be divided along racial lines: "If he was hoping to do that, he chose the wrong city.
"He chose the wrong group of people, it [the city] has come together in a remarkable way, in many ways due to the strength of the Christian community here in Charleston - black and white."
He added that: "One of the things that is an aspect of life here in Charleston is that black and whites live much closer together here and know one other more than in other parts of the country.
"But there's always room for improvement there."
Listen to Premier's Hannah Tooley speak to Bishop Robert Guglielmone here:
Listen to Premier's Desmond Busteed speak to Bishop Mark Lawrence here:
