Despite Pearce's vocal opposition to secession, in May 1861 the Arkansas Secession Convention appointed Pearce as a brigadier general and assigned him command of the state militia's 1st Division. He took command of Fort Smith in June after the Confederate recommissioned the abandoned U.S. Army post. Brigadier General Pearce assumed command of the 1st Division and had the following units under his direct command: Brigadier General Pearce, who lived in Benton County, established the headquarters, 1st Division, Provisional Army of Arkansas at Camp Walker at Maysville. Thus when a Union army began operating around Springfield in Southwest Missouri, Pearce's state troops were nearby. Pearce's troops, which are referred to as a brigade of State Troops in the official accounts of the battle, numbered 2,234 troops. Pearce agreed to co-operate with Brigadier General Benjamin McCulloch and his force of about 8,000 other soldiers from several commands, to form a sizable force and immediately marched toward Springfield. On August 10, 1861, Brigadier General Nathaniel Lyon, the forceful commander of Union troops in Missouri, attacked the Confederates. The Battle of Wilson's Creek came to an abrupt and inglorious halt when the Union commander was killed. Leaderless and outnumbered five-to-one, the bluecoats fled the battlefield. The Arkansas troops played a role in winning the battle, but paid a heavy price for victory. Two Arkansas units suffered particularly heavy casualties. Colonel Thomas J. Churchill's 1st Arkansas Mounted Rifles counted 42 killed and 155 wounded out of 600 men. Colonel John Gratiot's 3rd Arkansas Infantry, State Troops suffered 109 casualties, including 25 killed, out of a force of 500 men. Pearce's brief and controversial command ended shortly after the battle when in August, Arkansas authorities attempted to transfer his brigade to Confederate service. Pearce's troops were polled as to whether they wanted to be transferred to Confederate command as had been arranged prior to the battle. Brig. Gen. Pearce actively campaigned against joining the Confederate States Army. Sources differ as to how many of these Arkansas state troops agreed to the transfer. It appears that few were willing to continue in either service. Several units signed petitions requesting that General Pearce be allowed to remain in command. By the end of September 1861, all organized state troops had either been transferred to Confederate command or mustered out of state service. From December 13, 1861, to the end of the war, Pearce served as a major in the Confederate Commissary Department in Arkansas, the Indian Territory, and Texas. On June 21, 1865, he was paroled in Houston, Texas. He then went to Washington, D.C. and secured a pardon from President Andrew Johnson.
Post-war career
Pearce returned to Osage Mills in 1867 to rebuild his home, mill, and store. In 1872 he left to teach mathematics at the University of Arkansas, resigning this position in 1874 and returning to Osage Mills. From 1870 to 1884 he was employed by a Kansas City wholesale house. Later he moved to Texas for his wife's health and worked as a land examiner. N. Bart Pearce died in Dallas, Texas, on March 8, 1894, at the home of his daughter-in-law. He is buried in Whitesboro, Texas.
