With the outbreak of the Civil War, Burnside offered his services to the Union. He was appointed as a Brigadier General of Volunteers and tasked with raising and training troops in Rhode Island.

Burnside led a successful expedition to North Carolina, capturing Roanoke Island and New Bern. This campaign boosted his reputation and earned him promotion to Major General.

Following the Battle of Antietam, President Lincoln offered Burnside command of the Army of the Potomac, but Burnside declined, believing he was not qualified for such a significant responsibility. McClellan retained command temporarily.

Lincoln again offered Burnside command of the Army of the Potomac after relieving McClellan. This time, Burnside accepted, despite his reservations.

Burnside's command of the Army of the Potomac culminated in the disastrous Battle of Fredericksburg. His frontal assaults against entrenched Confederate positions resulted in heavy Union casualties and a major defeat. The battle severely damaged his reputation as a commander.

Burnside attempted another offensive, known as the 'Mud March', but it was thwarted by inclement weather and logistical problems. This further eroded his standing with the army and the Lincoln administration.

Following the Fredericksburg debacle and the 'Mud March', Burnside was relieved of command of the Army of the Potomac. He was replaced by Major General Joseph Hooker.

Burnside was transferred to command the Department of the Ohio, a less prominent role. He focused on suppressing Confederate sympathizers and maintaining order in the region.

While commander of the Department of the Ohio, Burnside arrested Clement Vallandigham, an anti-war Democrat, for making speeches against the war effort. This action caused considerable controversy and raised questions about civil liberties during wartime.

Burnside commanded Union forces during the Siege of Knoxville, successfully holding the city against a Confederate assault led by General James Longstreet. This victory helped restore some of his reputation.

Burnside participated in the Overland Campaign and the Siege of Petersburg. His performance during the Battle of the Crater, where Union troops attempted to break through Confederate lines by detonating a mine, was heavily criticized. He was subsequently relieved of field command.

Burnside was present at the surrender of General Robert E. Lee at Appomattox Court House, marking the end of the Civil War. He resigned his commission in the Union Army in June 1865.