But the outpouring of grief after a racist gunman killed nine African-Americans last week during a Bible study at a historic Charleston church is testing whether the longtime standoff can last.
After imagery emerged over the weekend of confessed killer Dylann Roof embracing the flag, local activists and some elected officials are pressing for its removal from the Capitol grounds here. And with national attention focused on the state's fraught -- and often racially-tinged -- politics, they think they might finally win.
"If we are going to do anything about it, it has to be now," said Boyd Brown, a former state representative who spoke at an anti-flag rally that attracted about 1,500 people this weekend. "You've got to keep this going. It's not just going to be hashtags."
The flag debate is quickly becoming a major political issue ahead of the state's crucial first-in-the-South presidential primary next year. Many Republicans, including Mike Huckabee and Rick Santorum, have avoided taking a position on the flag, though Jeb Bush highlighted his role in removing the flag from Florida's Capitol in 2001. Democratic frontrunner Hillary Clinton forcefully called on Americans to discuss racial divisions but hasn't weighed in specifically on whether South Carolina should remove the flag from the Capitol complex.
Gov. Nikki Haley, who has said the issue is worth a conversation, is under pressure to convene a special session to take up the flag question. That's unlikely to happen but Republican state Rep. Doug Brannon has already committed to introducing a bill to remove the flag when the legislature convenes in January.
That effort will face stiff headwinds.
As part of a compromise in 2000, lawmakers agreed to remove the Confederate flag
from the top of the Capitol dome and place it across the street while also adding a monument to African-Americans. But the legislation mandated that only a supermajority of the legislature could change that set-up going forward.
Privately, state lawmakers doubt Brannon's ability to attract enough Republicans to his side because he's not a member of the leadership. Brannon said that he has talked to two dozen Republicans in the lower chamber and they reacted positively, with some offering to sign on as co-sponsors. But he admitted that he hasn't thought much about how to piece together two-thirds of both houses to pass the bill.
"Right now my strategy is to scream a lot because my friend is dead," Brannon told CNN, referring to state Sen. Clementa Pickney, the pastor of the Charleston church who was among those killed. "Sen. Pickney's death and the death of eight others, that has to move us to do the right thing."
In an interview Sunday with CNN's Poppy Harlow, Brannon said he has long believed the flag should be in a museum. When asked why he hasn't done anything on the issue until now, he responded "I didn't do my job."
But what will matter more in the renewed flag fight is not the raw and complex emotions in the wake of the killings, but something much more simple--math.
"I appreciate the rally, but it has no impact on the legislative process," said state Sen. Darryl Jackson, a Democrat who helped hammer out the 2000 compromise. "The politics of the flag are the politics of the primary voter."
From his church pulpit on Sunday, Jackson urged patience on the flag issue, saying later that it could be interpreted as disrespectful to the dead to turn so quickly to politics.
"People are saying let's get some action now, but I don't want to alienate people I will need for a compromise," he said. "If we don't get a bi-partisan concensus, we will be fighting for the next 100 years."
There is a framework for such efforts. South Carolina lawmakers forged a bipartisan agreement this year on body camera legislation after the shooting death of Walter Scott by a white police office.
"This will not be done in a knee-jerk fashion," said Marlon Kimpson, a Democratic state representative. "I'm going to be in focus groups with business leaders and talking to constituents. The massacre opened up an opportunity but to build a super majority will require a lot of work."
The politics of the flag are complicated in South Carolina. A November poll from Winthrop University found that 73% of whites in the state want the flag to remain where it is. The same poll reported that 61% of blacks want it taken down.
"If we look at what the Confederate flag
meant in the past, you can't help but feel negative thoughts, especially now," said 24-year-old Meghan Delaney. "It should have been taken down a long time ago. If not now, when?"
For some whites, many of whom can trace their ancestry back to the Civil War, the flag represents heritage and pride.
"It's a symbol of family and my ancestors who defended the state from invasion. It was about standing up to a central government," said Chris Sullivan, who is a member of the Sons of the Confederacy. "The things that our ancestors fought for were not novel and they really are the same issues we have today."
But on the Capitol grounds just a few hundred feet from the Confederate flag
, activists over the weekend vowed to reclaim "southern pride" as inclusive and emblematic of a new, more diverse region where the "stars and bars" have no place.
"This heritage is hate," read one sign.
"Yep, it's racist," read another.
While there has yet to be a visible push-back from proponents of the flag, they are quietly reaching out to lawmakers. One worry among proponents is that taking down the flag would open up other monuments to scrutiny.
The flag is just one of several monuments that includes a statue of one-time segregationist Sen. Strom Thurmond and Ben Tillman, who sought to disenfranchise black citizens while he was governor. A stone marks the site of the state house before Sherman's troops burned it the ground during the Civil War.
"What's the difference between the flag and the monument," Sullivan asked. "That's what people are upset about now, but what about later?"