HATTIESBURG, Miss. — A small group has been gathering for almost four years — 203 consecutive Sundays, to be precise — at the front gates of the University of Southern Mississippi where three flags fly high.

The group has no problem with the Stars and Stripes, which sits atop all three flagpoles, but the protesters say one flag should have a different pattern.

“History is history,” said Joe Barnes, 67, one of the group’s stalwarts. “When I’m at home, I fly my Confederate flag, my Mississippi state flag and my U.S. flag.”

The Mississippi state flag flies neither at the University of Southern Mississippi nor since November 2016 at any of the Magnolia State’s other eight public institutions of higher learning.

After a racist gunman killed nine black worshippers at a South Carolina church in 2015, flags with an “X” pattern of stars that once marked the Confederate army’s fight for a slavery society were taken down.

Mississippi is the last holdout. Voters thought they had laid the issue to rest with a 2001 referendum, but calls to change the state flag came roaring back after the Charleston killings.

One by one, university presidents started rolling up the controversial banners. They said the Mississippi flag was incompatible with the diverse, inclusive community they hoped to establish on campus.

“This is a painful decision in many respects because this is a highly charged emotional issue for many people,” Delta State University President William N. LaForge said in November 2016 when his school became the last of the state’s eight colleges to lower the Mississippi banner.

“But in the absence of state action, we are making a decision I believe is right and just on all levels,” he wrote. “The objectionable portion of the state flag — the stars and bars — presents a polarizing symbol that is a barrier to progress and improved understanding of our state, our university, and our people.”

The state flag flies over the capital in Jackson and state government buildings, but at least 30 cities and counties have joined the universities in furling the flag, said Lea Campbell, founder and president of the Mississippi Rising Coalition, a social justice group with headquarters in Ocean Springs.

Voters will have another chance to speak on the issue, albeit obliquely, in November when they choose a new governor. Outgoing Gov. Phil Bryant, a Republican, has said any change to the flag should be put to a statewide vote and not be made by a coalition of officials in Jackson.

Tate Reeves, the lieutenant governor who will represent the Republican Party in the election, has the same view.

His Democratic opponent, Attorney General Jim Hood, did not respond to multiple attempts for comment but released a statement in April saying he supported changing the flag.

Such unwillingness to engage in debate on the topic is typical in state politics, The Clarion-Ledger reported that month when it took an impromptu survey of various candidates.

The protesters at the University of Southern Mississippi say politicians are dodging the issue. The No State Flag/No State Funds group noted that 65% of voters supported keeping the current flag in 2001.

That was years before Dylan Roof’s racist killings in Charleston, but Mr. Barnes and others said they have no problem with another referendum.

They tried to weave the flag into the state Constitution with Initiative 62 starting in 2017, but they were never able to amass enough signatures.

The Legislature has floated various bills that would change the flag, although none has ever reached the governor’s desk. A measure to fine universities that refuse to fly the flag failed in 2017.

For many weeks after beginning their protests, No State Flag/No State Funds attracted large and largely hostile crowds that pitted some faculty members, students and out-of-state activists against the pro-flag group.

The university has erected wooden barriers separating the sides, and an ongoing court case involves an anti-flag protester who sprayed pepper spray into the eyes of pro-flag demonstrator David Flynt.

Protesters insist they are far from the caricature of Klansmen in which they are often depicted.

Still, they make their allegiances clear. Mr. Barnes sports a “Make Dixie Great Again” red cap, and several of the protesters wear shirts emblazoned with some form of the Confederate symbol.

“No, I do not,” Mr. Barnes declared when asked whether he considered himself racist. The half-dozen others sitting under a tent on a scalding September afternoon echoed his response.

The group plants state flags of various sizes along the curb in front of them, and passing motorists sometimes honk or, as Robert Ulmer noted, present the group “with a thumbs-up or a middle finger. About 50/50.”

Mr. Barnes is retired from 18 years of active duty in the U.S. Army, and fellow protester Jessie Sanford said the universities’ decision is insulting not just to the Sons of Confederate Veterans, of which many protesters are members, but also the current military.

“I carried that flag when I served in Afghanistan with the Mississippi National Guard in 2011 and 2012,” Mr. Sanford said. “So I think it is disrespectful to all veterans.”

The Civil War hovers over the Deep South in ways unfamiliar to the rest of the nation. Hattiesburg sits in the middle of Forrest County, named after the general and KKK founder Nathan Bedford Forrest, a man so racist that he once participated the killings of wounded black U.S. soldiers on an apocalyptic Civil War battlefield in Tennessee. The state flag flies at a welcome center near Picayune over a memorial erected to “the Hancock Rebels,” who eventually served under Forrest in the Confederate army.

“I’m hoping the issue comes up in the [gubernatorial] debate,” Ms. Campbell told The Washington Times. “We’re certainly calling for it to be an issue, and we believe it is one voters want to hear about.”

Her group, Mississippi Rising, runs the #TakeItDownMs social media campaign as well as a YouTube presentation of Mississippians talking about why they believe the flag should be changed.

Ms. Campbell pointed to her group’s internal polling that she said showed a thin 51% majority in favor of changing the state flag for the first time in 2018.

The state does have a substitute design. The Stennis flag features one large blue star encircled by 19 smaller blue stars and flanked by red bands that represent the blood spilled by Mississippi veterans.

As the only state left in the union with the Confederate saltire, Mississippi is holding itself back economically as well as morally, Mississippi Rising says.

“The Confederate emblem has been used since the Civil War to represent various groups, including the army and government of the Confederate States of America and numerous white supremacist groups, as a symbol of white supremacy,” the group says. “Unspeakable acts of terror and violence against African Americans, Jews, LGBT citizens, immigrants, Catholics and other minorities have been committed by these groups under the Confederate emblem, and it is unacceptable that the flag representing our state enshrines the symbol of hate and flies on tax-payer-funded public properties.”

To Kimberly Craven, one of the No State Flag/No State Funds founders, the flag contains history good and bad and her alma mater should not make a unilateral decision that clashes with the will of taxpayers who keep the university afloat.

“I think in terms of our end goal maybe we haven’t accomplished that much,” Ms. Craven said. “But I think in terms of raising the issue and having people see the flag, it’s been good for the community.”

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