When the Civil War broke out, General Kimball was the captain of the local militia company, the Fitchburg Fusiliers, of which his father was a charter member and first lieutenant after organization. General Kimball himself joined the company at the age of eighteen and had risen from the ranks through the various offices of the company, and was a faithful and conscientious officer from the very first. His company maintained a high standard of efficiency. He tendered his company to Governor Andrew to serve in the war, January 1861, and his company with Companies A, and C, of the old Ninth Regiment, became the nucleus of the famous Fifteenth Massachusetts Volunteers under Colonel Charles Devens. The Fitchburg Fusiliers had also been a part of the Ninth Regiment, M. V. M. [Massachusetts Volunteer Militia] as Company B. He had been adjutant of the regiment from May 1, 1858, to January 7, 1860. Before leaving the state he was commissioned, August 1, 1861, major of the regiment, and became lieutenant-colonel April 29, 1862. As lieutenant-colonel of the Fifteenth, he commanded the regiment in all the battles of the Peninsular campaign, siege of Richmond, Second Bull Run, South Mountain, Antietam, and down to Fredericksburg. In the battle of Antietam alone the regiment lost in less than 20 minutes 330 killed and wounded and fourteen missing - 344 out of 606 officers and men, including First Massachusetts Sharpshooters attached to the regiment. His horse was shot under him. The Fifteenth was attached to the First Brigade, Second Division, Second Corps, Army of the Potomac. In November, 1862, Colonel Kimball was called from the front to take command of the Fifty-third Regiment.
He commanded that regiment in 1863 in the Department of the Gulf, and was at the siege of Port Hudson. In the assault of June 14, 1863, he was dangerously wounded in the thigh, but did not leave the field until after the fighting was over. His regiment was in the Third Brigade, Third Division, Ninteenth Army Corps, Department of the Gulf. An attack of malarial fever prostrated him, and he returned to Worcester county to serve as superintendent of recruiting there. In the winter of 1864 he organized the Fifty-seventh Regiment in Massachusetts. He was brevetted brigadier-general March 13, 1865, "for gallant and distinguished services in the field during the war." He was in the service nearly three years.