Bartow was also a colonel in the Georgia Militia commanding the 21st Oglethorpe Light Infantry during the early months of the American Civil War.

Bartow was a delegate from Georgia's 1st congressional district to the Southern Convention in Montgomery, Alabama becoming an inaugurating member of the Confederate Provisional Congress—leading efforts to prepare local forces in the aftermath of secession, protracting into The American Civil War of 1861–65.

Colonel Bartow was killed at the First Battle of Manassas, becoming the first brigade commander of the Confederate States Army to die in combat.

While at Franklin, Bartow was a member of the Phi Kappa Literary Society and was mentored by John M. Berrien, a U.S. senator and former Attorney General in Andrew Jackson's administration.

Bartow was subsequently employed by the Bryan Superior Court and admitted to the State Bar of Georgia soon after his return to Savannah.

The following year, he was elected as captain of Savannah's 21st Oglethorpe Light Infantry, a reserve guard company that had been formed in 1856.

On May 28, 1861, elections were held to select representatives to the convention, and Bartow emerged as a delegate, along with John W. Anderson and A. S. Jones.

Bartow was subsequently chosen to represent Georgia in the Provisional Congress of the Confederate States at Montgomery, Alabama, starting February 4, 1861.

However, his plans were blocked by Governor Brown, who had already decided to concentrate the state's armed forces strictly for the defense of Georgia.

Bartow appealed personally to the Confederate President, Jefferson Davis, using a new law authored by Louis T. Wigfall of Texas that authorized any citizen to offer any voluntary military force directly, without state mediation, to the Confederate President, who would also determine its military leader.

Among other things, he alleged that Bartow was seeking his own glory by assuring a high command and aspiring to a promotion to colonel.

He also alleged that Bartow had written the law beforehand, tailoring it for his own plans and forcing Davis to ignore the authority of the Confederacy's "independent" states.

[citation needed] Nonetheless, Bartow arrived in Savannah on May 21 to assemble his 106 soldiers and to arrange for a train to take them to Virginia's battlefront.

A great rally of cheerful citizens congregated at the station, accompanied by the remaining local militia, which fired an artillery salute in Bartow's honor.

Bartow defended himself vehemently, countering each of the personalized attacks and stating that he had undertaken the current campaign under the sole command of Jefferson Davis.

"[citation needed] Bartow's 21st Oglethorpe Light Infantry finally arrived in Richmond, Virginia, with the objective of protecting the region from any Union attack.

Late in June 1861, Bartow received orders to move his troops to the outskirts of Manassas to support General P. G. T. Beauregard.

One of the survivors later wrote, "Practically half of the Eighth's 1,000 Georgians fell dead or wounded, or were captured or lost ... Bartow led his men to an exposed eminence which was too hot to hold."

When notified of Bartow's death, the Provisional Congress adjourned its sessions "in testimony of [its] respect for his memory", as expressed by its spokesman, T. R. R. Cobb.

The chamber felt an "unfeigned sorrow" due to the "heavy loss sustained by the Confederacy in the death of one of her most efficient counselors."

His granite monument has two of his historical phrases engraved under a wreath and a saber: "I go to illustrate Georgia" and "They have killed me, boys, but never give up."

After the battle, on the approximate spot where Bartow was killed, Confederate soldiers placed a small stone landmark (engraved in Savannah) which quoted his last words: "My God, boys, they have got me, but never give up the field."

After years of postponement due to the war and its effects, on February 7, 1890, the Savannah City Council approved erecting a memorial recognizing native sons Francis Bartow and Lafayette McLaws.

The Georgia General Assembly recently acknowledged the work of this organization, citing them "for their role in protecting and preserving Confederate heritage" (LC 21 7026, House Resolution 1524).