In 1860 Cleburne formed a militia company in Helena that was more a social organization than military. He was elected captain of this company, the Yell Rifles. After the firing on Sumter he took his company to a training camp north of Memphis. Companies were combined and he was elected colonel of the newly formed 1st Arkansas. In Little Rock the state government appointed two generals to handle Arkansas troops, one for the eastern part of state and one for the western part. Thomas Bradley proved to be a poor general and after a disastrous scouting expedition Cleburne placed Bradley under virtual arrest (there was a guard around the general's tent and Cleburne refused to accept any orders from him). Cleburne allowed Bradley to leave the camp if he resigned, which he did and then went to Little Rock to seek a court martial against Cleburne. Bradley though had second thoughts, figuring the court martial would expose his own short comings and so instead turned the whole matter over to Gideon Pillow. Pillow did not want the headache and let the whole matter end quietly.
Jefferson Davis soon put a national commander into Arkansas, William Hardee. Hardee knew of the Bradley situation and so went to the governor first. The governor agreed to have Hardee in command if he would allow the Arkansas troops to vote whether they wanted to be transferred into national service or to serve as home guard only. Hardee reluctantly agreed. Cleburne liked Hardee right from the start and campaigned hard for the men to accept the transfer. 1800 of 3000 men in the camp voted for the transfer but 8 of Cleburne's 10 companies agreed to it. In June the camp was moved to a spot near the Missouri border on the Black River.
While a hard commander Cleburne also cared for his men's well being and came to be liked and respected. He was not just a commander but a leader.
After Polk broke Kentucky's neutrality Albert Sidney Johnston ordered Hardee's force to reinforce Bowling Green. They arrived there in October and Johnston soon made Hardee a division commander, Buckner was the other division commander. Hardee nominated Cleburne, Hindman and RG Shaver to command his three brigades. Cleburne's brigade consisted of the 1st Arkansas, 5th Arkansas, 6th Mississippi and 5th Tennessee.
On February 7, Johnston and Beauregard decided to abandon Bowling Green. March 4, Cleburne received official notification of promotion to brigadier general.
At Shiloh Cleburne commanded a brigade of six regiments and a battery. Three of his regiments had served with him previously; the 1st Arkansas had been redesignated the 15th Arkansas and the 5th Tennessee had also been redesignated the 35th Tennessee, while the 6th Mississippi remained. Cleburne also gained Bate's 2nd Tennessee, 23rd Tennessee, 24th Tennessee and Trigg's Battery. His brigade was one of three brigades in Hardee's "corps". The other two brigades, RG Shaver and Sterling Wood, were under the command of Cleburne's old friend Hindman.
On the march to Shiloh Cleburne's was the first brigade to leave Corinth, starting out about noon on April 3. That evening he took a side road to be near a spring but left no one in his rear to inform anyone else. When he returned to the main road in the morning he found it blocked by Polk's corps. Polk moved aside so Cleburne could pass but much time was lost in this enterprise. Luckily the entire army was behind schedule so Cleburne's problems were not too glaring. By dawn of April 5 Cleburne (and Hardee) were in position but Bragg and Polk were not. Cleburne formed Hardee's left flank and Bate's 2nd Tennessee was the extreme left of the army. On April 5 they had a small skirmish with a Union cavalry patrol, even fired off some artillery, but the Union high command ignored all signs of the Confederate advance.
In the early morning of April 6 Cleburne's attack took him into the swamp along Shiloh branch. The swamp formed a wedge in his lines sending the 6th Mississippi and 23rd Tennessee to the right and the rest of the brigade to the left. Initially he stayed with his right regiments but when their assault sputtered he detoured around the swamp to find the rest of the brigade. In the meantime they had been torn to tatters. Seeing he could do little there he went back around the swamp to his right regiments. While they were vastly depleted he did order another attack which finally pushed the Ohio troops out of the way. This contingent was so depleted that he ordered them to the rear for rest. On his way back to the left he received orders from Hardee (or perhaps saw Hardee directly) to go to the rear and round up stragglers from the captured camps. After a few hours of this proved useless he went off to find his other regiments. The 24th and 35th Tennessee were in the best condition and so he attacked with them and was able to drive the Union back, though this retreat was mostly due to other Union retreats along the line. It appears that at dusk Cleburne was near Cloud Field on the left of the Confederate advance.
For the second day only 800 of 2700 men answered roll call. It is not clear where he fought but appears that he was near the Davis Wheatfield. Late in the day Bragg ordered him to attack, an attack he thought was foolhardy but did anyway. The results were disastrous and he blamed Bragg for the loss, not the last time he would blame Bragg for the army's woes. As he left the field that day only 58 men of his brigade were with him. Nearly every officer in the brigade over the rank of captain was dead or wounded. In hindsight he should have given temporary command of his two right regiments to Hindman on the first day. Hindman would then have been able to coordinate their attacks and perhaps broken that Union line earlier. He could then have devoted all his focus to his other four regiments and perhaps done better with them. His attacks, three frontal charges, lacked creativity but he was hampered by terrain.
When the losses were counted later, after stragglers had reappeared, his losses in killed, wounded and captured amounted to 1043 of 2750, 38%. The 6th Mississippi lost 300 of 425 men, the fourth highest percentage loss by any unit in the entire war. The 15th Arkansas was so depleted that they were consolidated with the 13th Arkansas. Lucius Polk was elected the lieutenant colonel of the 13-15 Arkansas. Polk was a former member of the Yell Rifles, a friend of Cleburne's and also nephew of corps commander Leonidas Polk, the bishop. The commanders of the 2nd Tennessee, William Bate, and 35th Tennessee, Benjamin Hill, were wounded and would return to command. Other vacancies were filled by elections.
During April Cleburne decided to have shooting contests and pick the 5 best shots in each company to create sharp shooter companies. In his unique command style he went to each regiment to explain his idea to the men before implementing it. He wasn't shying away from charges he just wanted to better the odds before a charge, especially when it came to dealing with artillery.
While in Corinth he had only one occasion when he met the enemy, May 28 at Farmington. They were out on a patrol when the 35th Tennessee (with Cleburne) ran into a Union division. He rode off to get support and found the 24th Tennessee blocked by a small creek. He chewed out Colonel RD Allison and got the regiment in position but as soon as he left them they ran. He then found the 2nd Tennessee and 48th Tennessee and got them into position but orders then arrived from Hardee reminding him that since he was not to bring on an engagement that he should now withdraw. Afterwards he relieved Allison of command and placed Major Hugh Bratton in command. That night Beauregard decided to evacuate Corinth (the decision had nothing to do with Cleburne's engagement). During the night of May 29-30 the Confederates left Corinth. First they went to Baldwin for a week and then to Tupelo. On June 14 Beauregard took a leave of absence and Bragg took command, but Davis soon made the command change permanent.