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At first, Hayes was not in favor of going to war to preserve the Union, even when the Southern states began to secede after Lincoln's election in 1860. Hayes suggested at first that the Union should just, in his words, "let them go." This was in keeping with local political sentiment. Although Ohio had voted for Lincoln in 1860, Cincinnati voters turned against the Republican party after southern states began to secede and the Democrats and Know-Nothings combined to sweep the city elections in April 1861. Hayes lost his position as city solicitor of Cincinnati.
After the Confederates had fired on Fort Sumter, Hayes reconsidered the question of war and joined a volunteer company. It was largely composed of his friends from his literary society. In June, 1861, Governor William Dennison of Ohio appointed several of the officers of the volunteer company to positions in the 23rd Regiment of Ohio Volunteer Infantry. Hayes was promoted to major. Also joining the regiment as a private was another future president, William McKinley.
After a month of training, Hayes and the 23rd Ohio set out for western Virginia in July 1861 as a part of the Kanawha Division. They spent the next few months out of contact with the enemy until September, when the regiment encountered Confederates at Carnifex Ferry in present-day West Virginia and drove them back. In November, Hayes was promoted to lieutenant colonel. He led his troops deeper into western Virginia, where they remained for the winter. The division resumed its advance the following spring, and Hayes led several raids against the rebel forces. In September of 1862, Hayes's regiment was called east to reinforce General John Pope's Army of Virginia at the Second Battle of Bull Run. Hayes and his troops did not arrive in time for the battle, but they joined the Army of the Potomac as it hurried north to cut off Robert E. Lee's Army of Northern Virginia, which was advancing into Maryland. Marching north, the 23rd was the lead regiment encountering the Confederates at the Battle of South Mountain on September 14.
Hayes led a charge against an entrenched position and was shot through his left arm, fracturing the bone. The regiment continued on to Antietam, but Hayes was out of action for the rest of the campaign. In October, he was promoted to colonel and assigned to command of the first brigade of the Kanawha Division as a brevet brigadier general.
Hayes' division spent the following winter and spring near Charleston, Virginia (present-day West Virginia), out of contact with the enemy. Hayes saw little action until July 1863, when the division skirmished with John Hunt Morgan's cavalry at the Battle of Buffington Island. Returning to Charleston for the rest of the summer, Hayes spent the fall encouraging the men of the 23rd Ohio to re-enlist, and many did so.
In 1864, the Army command structure in West Virginia was reorganized, and Hayes's division was assigned to George Crook's Army of West Virginia. Advancing into southwestern Virginia, they destroyed Confederate salt and lead mines there. On May 9, they engaged Confederate troops at Cloyd's Mountain, where Hayes and his men charged the enemy entrenchments and drove the rebels from the field. Following the rout, the Union forces destroyed Confederate supplies and skirmished with the enemy again successfully.
Hayes and his brigade moved to the Shenandoah Valley for the Valley Campaigns of 1864. Crook's corps was attached to Major General David Hunter's Army of the Shenandoah and soon back in contact with Confederate forces, capturing Lexington, Virginia on June 11. They continued south toward Lynchburg, tearing up railroad track as they advanced. Hunter believed the troops at Lynchburg were too powerful, however, and Hayes and his brigade returned to West Virginia. Hayes was critical of his commanding general, writing in a letter home that "General Crook would have taken Lynchburg."
Before the army could make another attempt, Confederate General Jubal Early's raid into Maryland forced their recall to the north. Early's army surprised them at Kernstown on July 24, where Hayes was slightly wounded by a bullet to the shoulder. Hayes also had a horse shot out from under him, and the army was defeated. Retreating into Maryland, the army was reorganized again, with Major General Philip Sheridan replacing Hunter. By August, Early was retreating down the valley, with Sheridan in pursuit. Hayes's troops fended off a Confederate assault at Berryville and advanced to Opequon Creek, where they broke the enemy lines and pursued them farther south. They followed up the victory with another at Fisher's Hill on September 22, and one more at Cedar Creek on October 19. At Cedar Creek, Hayes sprained his ankle after being thrown from a horse and was struck in the head by a spent round, which did not cause serious damage. Hayes's conduct drew the attention of his superiors, with Ulysses S. Grant later writing of Hayes that "his conduct on the field was marked by conspicuous gallantry as well as the display of qualities of a higher order than that of mere personal daring."
Cedar Creek marked the end of the campaign. Hayes was promoted to brigadier general in October 1864 and became a brevet major general. The army went into winter quarters once more, and in spring 1865 the war quickly came to a close with Lee's surrender to Grant at Appomattox. Hayes visited Washington, D.C. that May and observed the Grand Review of the Armies, after which he and the 23rd Ohio returned to their home state to be mustered out of the service.
Although Hayes' military service was motivated by a sense of bravery and patriotism, it didn't hurt his political career. He didn't even have to campaign to win election. While serving in the Army of the Shenandoah in 1864, Hayes received the Republican nomination to the House of Representatives from Ohio's 2nd congressional district. He was asked by friends in Cincinnati to leave the army to campaign, but Hayes refused, saying that an "officer fit for duty who at this crisis would abandon his post to electioneer for a seat in Congress ought to be scalped." Even without campaigning in person, Hayes wrote several letters to the voters explaining his political positions and was elected by a 2,400-vote majority over the incumbent Democrat, Alexander Long.