Dylann Roof was convicted last month of 33 federal charges, including hate crimes, after opening fire on a Bible study group in 2015.
He remained unrepentant and had told the jury: "I felt like I had to do it and I still feel like I had to do it."
The jurors deliberated for nearly three hours before reaching their verdict.
The massacre shocked the nation and reignited a debate about race relations and the flying of the Confederate flag.
Roof told police he wanted to start a race war and he was photographed holding the battle flag, which to many is a symbol of hate.
The tragedy led to the flag being removed from the South Carolina statehouse, where it had flown for 50 years.
Earlier on Tuesday, Roof addressed the jury, saying: "I don't know what good it would do anyway" if they spared his life.
The judge will issue a formal sentence on Wednesday morning.
After the sentence was announced, the 22-year-old killer stood and requested to be appointed new lawyers and to file for a retrial.
US District Judge Richard Gergel replied that he was "strongly disinclined" and instructed Roof to think about it overnight.
Nearly two dozen friends and relatives of those gunned down at the Emmanuel AME Church in Charleston testified during the sentencing phase about how Roof's crimes have affected their lives.
But none of them had appealed to the jury to return a death sentence.

Babur Karamat Raja, 41, from Sutton Coldfield is accused of attacking the 40-year-old in Sutton Coldfield on Friday.
He has also been charged with assault, attempt child destruction and possession of a knife.
Mr Raja is due to appear before Birmingham magistrates on Monday.
Police said the woman is in a stable condition in hospital and her baby girl - born following the alleged attack - continues to do well.
The victim's family praised five men who went to her aid before paramedics arrived.
In a statement released by police, they said: "We'd all like to express our heartfelt thanks to everybody who helped her on Friday afternoon.
"Your fearlessness and selfless actions saved both their lives and we are overwhelmingly grateful to you all."

A report from Bristol City Council found vinegar was more expensive and less effective than glyphosate.
Contractors were also unwilling to use vinegar as they were afraid of residents' complaints about the smell.
But a local councillor says potential health concerns should take a higher priority.
The council started a year-long trial in 2016 to see how effective vinegar would be in replacing glyphosate, following pressure from campaigners who fear it can cause cancer.
The World Health Organisation and the Food and Agriculture Organization of the United Nations have, however, decided that food grown with it is unlikely to cause harm to human health.
In the report out this week, the cost of using vinegar was found to be 3.6 times greater than glyphosate, and weeds treated by vinegar would reappear within a month instead of five to six months after being sprayed with the chemical weed-killer.
Contractors added they were not willing to recommend the use of vinegar and "were concerned that complaints about its 'smell' would harm their reputation".
Councillor Anthony Negus said the trial "must be redone much more rigorously", describing the report as "patchy".
"Cost has to be a minor factor. If there is a real risk to health, that trumps everything," he said.
Community gardener Karen Sillence called on the council to "mobilise the public to help".
"There have to be other ways they haven't tried to clear weeds without using chemicals. I want to see them persevering."
A Bristol City Council spokesman said the authority would "now consider our options and continue to keep up to date with relevant research and emerging products and techniques, to see if we can find a better solution".
A white supremacist has been sentenced to death for the racially motivated killings of nine black people at a South Carolina church.
[NEXT_CONCEPT]
A man has been charged with two counts of attempted murder after a pregnant woman was stabbed in a West Midlands street.
[NEXT_CONCEPT]
Campaigners have urged a city council not to give up on using vinegar instead of controversial chemicals to kill weeds on its streets.