In June 1861, Kimball received a position as colonel of the 14th Indiana Infantry. He served at the battle of Cheat Mountain and, the following year, at the Battle of Kernstown. His success at Kernstown inspired his promotion to brigadier general in April 1862. He led his brigade through the Battle of Antietam and at the Battle of Fredericksburg, where he was wounded. In the summer of 1863, he served in the western theater at the siege of Vicksburg. In the Atlanta campaign, he distinguished himself at the Battle of Peachtree Creek, after which he received command of a division. Later he was involved in the Franklin-Nashville campaign. He was brevetted as a major general in 1865 at the end of the war.