Reverends Al Shapton (2nd R) and Jesse Jackson (C) stand behind the casket holding Emanuel AME Church shooting victim Ethel Lance during her funeral at the Royal Missionary Baptist Church in North Charleston, South Carolina, June 25, 2015. PHOTO AFP
Obama will deliver the remarks for pastor Clementa Pinckney, who was gunned down along with eight other African Americans during Bible study in a historic church nine days ago.
The shooting was allegedly carried out by Dylann Roof, 21, a white supremacist.
The carnage renewed discussions of racism and hate groups in America and led to a furor over the controversial Confederate flag, which is present throughout the south but that many see as a symbol of racism.
For Obama, the shooting touched a particular nerve because it overlapped with two thorny issues in his presidency: gun control, which he never managed to overhaul, and racial divides.
Soon after the killings, a frustrated and angry Obama condemned the country's lack of action over mass shootings.
Several thousand people, including Vice President Joe Biden, are expected at the ceremony at a university in Charleston near the Emanuel African Methodist Episcopal Church where the shooting took place.
Mourners held the first funeral services Thursday for some of the nine African Americans killed.
Hundreds filed past the open coffin of Ethel Lance, 70, at a funeral home in North Charleston, ahead of an afternoon service for Sharonda Singleton, 45.
Read: With heavy police presence, Charleston mourns after church massacre
Pallbearers carry the casket of Rev. Clementa Pinckney into a memorial service at the Emanuel African Methodist Episcopal Church on June 25, 2015 in Charleston, South Carolina. PHOTO AFP
Emotions ran high at the Royal Missionary Baptist Church as friends and relatives bid a final farewell to Lance, a custodian at a Charleston arts center.
"I am here to tell you that we are stronger because we are together as a community," Reverend Norvel Goff told the mourners, the local Post and Courier newspaper reported.
Lance was later laid to rest at the Emanuel cemetery, where her children and grandchildren kissed her coffin and well-wishers threw roses into her grave.
Singleton, a speech pathologist, high school track coach and pastor at Emanuel, was remembered by a capacity crowd at the 2,000-seat Mount Moriah Missionary Baptist Church.
"She believed she could change every child," said South Carolina Governor Nikki Haley, who attended both funeral services.
Seen in the pews were Jesse Jackson and Al Sharpton, two of the most recognizable civil rights activists in the United States today.
Thousands pay respects
On Wednesday, thousands filed past Pinckney's open coffin at the South Carolina legislature in the state capital Columbia, where he had served as a senator.
Services for the other victims are scheduled throughout the weekend and into next week.
Meanwhile, the campaign against the Confederate battle flag flying outside the South Carolina legislature picked up steam.
Read: Website appears to show attack manifesto of Charleston shooting suspect
Adding his voice to the movement was College of Charleston president Glenn McConnell, a former Republican lieutenant governor and avid Civil War battle re-enactor.
Members of the St. Stephen A.M.E. Church of Jacksonville, Florida sing hymns outside the memorial service for Rev. Clementa Pinckney at the Emanuel African Methodist Episcopal Church on June 25, 2015 in Charleston, South Carolina. PHOTO AFP
As a state senator, McConnell favored positioning the flag alongside a Confederate memorial on the State House grounds 15 years ago.
"Today is a different time," he said, adding that the flag should come down as a "statement of courtesy and goodwill to all those who may be offended by it."
Some revere the Civil War-era flag as an emblem of Southern heritage, but others condemn it as a symbol of racial hatred and white supremacy.
Roof's getaway car -- he was arrested a day after the shooting in North Carolina -- bore a Confederate license plate, and photos later emerged online of him brandishing the flag together with a handgun. He reportedly hoped to trigger a race war with the shooting.
South Carolina Governor Nikki Haley, a Republican with Tea Party support, has come out in favor of removing the flag, but the final decision hinges on a vote by the state legislature.
Proliferation of petitions
MoveOn.org, a left-leaning campaign group, said more than 600,000 people have signed more than 50 petitions hosted on its website against the flag.
In Washington, US Attorney General Loretta Lynch said it was too early to say whether Roof will face federal civil rights charges.
A hate crimes investigation is unfolding, she said, but "it's simply premature at this point to be able to announce" how Roof might be charged.
South Carolina has charged Roof with nine counts of murder, one for each victim. He remains in solitary confinement at a North Charleston jail.
Haley has said that she favors the death penalty for Roof if he is convicted.
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