To start the Kentucky campaign Bragg gave two brigades to Kirby Smith, his best two brigades, Preston Smith and Cleburne. Cleburne reported to Kirby Smith on August 7 in Knoxville and was given command of both brigades as a division, command of Cleburne's brigade went to Hill.
Kirby Smith planned to use Stevenson's division to hold the Union at Cumberland Gap and then move into their rear with his other three divisions. Cleburne's division was the first one to march, leaving at dawn on August 14. They covered the 60 miles to Barboursville, Kentucky in 50 hours and were then on the Union supply line. Kirby Smith then abandoned the earlier plan of joining with Bragg in Tennessee and decided to march on Lexington alone.
On the afternoon of August 29 Cleburne's division was at Big Hill, south of Richmond. The Confederate cavalry was in front but soon broke under a Union cavalry attack. Cleburne repulsed this attack, capturing about 30 soldiers. That night he received orders to attack the next morning. In the morning he advanced about 1-2 miles to Mount Zion Church, six miles south of Richmond. He deployed Hill to the right of the pike with Preston Smith behind Hill. At 7:30 AM Kirby Smith arrived and decided to flank the Union with Churchill's division which was coming up. Meanwhile Cleburne's sharpshooters had been skirmishing with the artillery pretty effectively. After an hour Union General Mahlon Dickerson Manson decided to attack first and launched an attack on Cleburne's right flank. Cleburne decided that to do this the Union must have weakened their center so instead of responding to the attack by reinforcing the point of contact he launched an attack of his own on the Union center. He brought Preston Smith up to hold the right while he lead Hill forward. As he passed down the line he saw his friend Lucius Polk being taken to the rear. He stopped to see if Polk was okay and Polk responded that he was only slightly wounded. Cleburne started to reply but a bullet pierced his left cheek, knocked out two teeth and exited through his open mouth, he would later joke that he spat the bullet out. The swelling and bleeding soon prevented him from speaking so he turned command over to Preston Smith, the battle was mostly over when he did this. It ended up being the most complete Confederate victory of the war; 4300 Union soldiers were captured including General Manson. Among the captured supplies were many pair of blue pants which Cleburne's division was soon wearing.
Kirby Smith's part of active campaigning in Kentucky was nearly over, which gave Cleburne some time to heal. Eating and speaking were difficult. Shaving was also difficult and he soon sported a beard, which he kept after the wound completely healed. It also happened to cover the scar quite nicely. In late September Preston Smith and Cleburne's brigades were returned to Bragg's army and Cleburne returned to brigade command. On September 23 he rejoined his brigade at Shelbyville. Bragg ordered him to hold Shelbyville and if pressed to retreat towards Frankfort. On October 1 he retreated towards Frankfort as the Union advanced to within 5 miles of his position. The next day he received orders to join Polk's move towards Harrodsburg, where he would be able to rejoin Hardee's corps (would become part of Buckner's division).
October 8 found Cleburne at Perryville. At this time his brigade numbered about 1000 men, the 13-15 Arkansas was down to 200. At noon he was ordered to support Johnson's brigade northwest of town. Buckner formed his division about 2 PM in column, Johnson in front, then Cleburne and St. John Liddell in the rear. To the right was Cheatham's division and on the left was Patton Anderson. Johnson soon advanced and Cleburne was held in reserve until 4 PM. When Cleburne advanced he found Johnson in a creek bed, Johnson expressed determination to advance again but his men were out of ammunition. Cleburne would attack alone.
Cleburne noticed that the Union line was a bit back from the crest and could not shoot at his advancing men. He put a skirmish line with the colors forward of the main line by about 10 paces. When they crested the hill that line would take the brunt of the fire and Cleburne's brigade could then rush upon the Union before they could reload. This charge succeeded and drove the Union back. After driving them from this position he crossed the Mackville road and stopped in a cornfield. A battery on his left started to enfilade this position, wounding Cleburne in the leg (foot) and killing his horse. Cleburne then advanced on this battery and drove it from the field, ending up 75 yards from the new Union line, with both flanks exposed. Rather than retreat his 800 men held on here resisting counter attacks until Liddell's brigade came up near dusk.
At one point in the fight Confederate artillery had fired on Cleburne's brigade mistaking the blue pants for a Union line. It took a little convincing but the Confederate artillery did stop the bombardment. Symonds says that Cleburne demonstrated more courage than judgment during the campaign but it seems to me that he did use very good judgment at Richmond and Perryville. Cleburne blamed Bragg for the outcome of the campaign.
The army soon retreated to Knoxville, then to Chattanooga and finally to Murfreesboro. During the army reorganization Buckner was transferred to Mobile, opening up a division command in Hardee's corps. Buckner suggested Cleburne and Hardee readily agreed. It was a slightly odd promotion in that Sterling Wood and Bushrod Johnson were both his seniors within the division. Johnson and Wood had performed well in Kentucky; Johnson was also a West Point graduate; and both were native southerners. Cleburne did get the promotion to division command and his promotion to major general became official on December 12. His division consisted of four brigades; Wood, Johnson, Liddell and his old brigade, now under Lucius Polk. It does not appear that Wood or Johnson were upset about Cleburne being promoted over them.
He received other good news that winter. Sometime in November his youngest half brother, Kit, came down from Cincinnati. It is not clear if Pat refused him a position on his staff or if Kit never asked. In any event Kit decided to join Morgan's cavalry and make a name for himself.
The night before the attack Cleburne received his orders. His and McCown's divisions would lead the assault, supported by Polk's two divisions. That night his men crossed the cold Stones River and aligned for the attack by using the distant light from Cheatham's division's camps. Cleburne's men did not light any fires of their own so as to not reveal their location. The attack was to be made at dawn, which Cleburne estimated would be at 5 AM. At 4:30 AM he roused his command and arranged his division from left to right as Liddell, Johnson and Polk. Wood was placed in reserve behind Polk. When 5 AM came it wasn't light yet but Hardee sent Cleburne forward anyway. He was to follow McCown but McCown went too far to the left and Cleburne was unable to follow him. Eventually McCown got things back together and came up on Liddell's left.
Cleburne's men were able to knock through line after line and by 9 AM had reached the Wilkinson Turnpike. About this time they had advanced past Cheatham on their right and started to receive enfilading fire on their right. A half hour later the attack got rolling again, partly because McCown and Cleburne were now side by side. Together they presented a 10 brigade front which overlapped the Union right by a half mile. But now there were no Confederate reserves if the attack should falter.
Near the Nashville Pike Cleburne encountered the fifth Federal line. Around 3 PM they cracked this line and briefly held the turnpike, Rosecrans' line of retreat. A fresh Union line came up and drove Cleburne back from the turnpike. Cleburne wanted to attack again but wasn't sure if it was possible. He asked Johnson for advice and he replied that an attack would be "very hazardous." Then Cleburne asked Hardee if he should attack. Hardee knew that if Cleburne was having doubts then it was unwise to attack so he ordered Cleburne to hold his ground.
The next day Bragg ordered Cleburne to make a reconnaissance. Cleburne sent Liddell's brigade in but they soon needed help so he sent Wood in too. By the time Wood got there though Liddell had retreated and Wood found himself outgunned. The fighting cost 100 men from the division. The rest of the day was spent waiting for more orders. The third day, when the fighting kicked up in full force on the Confederate right, Cleburne's brigade saw no combat. On the morning of January 2nd Bragg held a conference and decided to retreat. That afternoon he held another conference asking if the army could stay 24 more hours to bring off the wounded. Cleburne said that he could hold for 24 more hours but most of the other generals said no and so the original plan of retreat remained.