Regiments were generally numbered and named for the state in which they were organized and from which most of their soldiers hailed (for example, 1st Virginia Infantry Regiment). Confederate brigades and divisions were generally named for their commanders, past or present (for example, the Stonewall Brigade), which often created confusing circumstances. During Pickett's Charge at the Battle of Gettysburg (1863), Pickett's division was commanded by George E. Pickett. But Heth's division, named for Henry Heth who was wounded on the first day of the battle, was commanded by J. Johnston Pettigrew, and Pender's division by Isaac R. Trimble. Confederate general A. P. Hill's Light Division, meanwhile, was actually the Army of Northern Virginia's largest division, with seven brigades.

The word "corps" was derived from the French term corps d'armee. Union general George B. McClellan first created Union corps in March 1862—there would be forty-three altogether, each designated by a number—and sometimes, as in the case of Ambrose E. Burnside's Ninth Corps, they moved from army to army as necessary. In 1863, Union general Joseph Hooker, in a literal attempt to increase the Army of the Potomac's esprit de corps, gave each Union corps its own special badge insignia. The Confederate Army of Northern Virginia was composed first of two, then of three corps, known sometimes by their numbers, sometimes by their commanders' names. Confederate general James Longstreet commanded the First Corps and Thomas J. "Stonewall" Jackson the Second Corps. After Jackson's death following the Battle of Chancellorsville (1863), Robert E. Lee gave Jackson's Corps to Richard S. Ewell and created a new Third Corps, putting it under the command of A. P. Hill. Richard H. Anderson briefly commanded a small Fourth Corps beginning in October 1864.

Most Civil War soldiers were volunteers (or conscripts) and not members of the Regular Army. Their regiments were temporary regiments of volunteers organized for the duration of the soldiers' enlistment. Some officers, however, did hold Regular Army commissions (especially, but not exclusively, those who had attended the United States Military Academy at West Point). As a result, a parallel system of rank developed in which a Union officer might be, for instance, a major general of volunteers but only a colonel in the Regular Army.

Pay, meanwhile, was usually doled out according to the higher of the two ranks. Because rank was sometimes awarded retroactively, there were sometimes pay disputes, as was the case with Winfield Scott, who famously demanded twenty years of back pay when, before the war, Congress backdated his promotion to lieutenant general to one of his famous Mexican War victories. The date of promotion was extremely important because both armies used seniority to distinguish between two officers of the same rank. During the Battle of the Crater (1864), Union general-in-chief Ulysses S. Grant was forced to issue separate orders to the head of the Army of the Potomac, George G. Meade, and Meade's practical subordinate, the Ninth Corps commander Ambrose Burnside. Grant's problem was that because of seniority Burnside technically outranked Meade and so resisted accepting orders from him.

Further confusing matters was a system of brevet ranks. Neither army awarded medals; instead, they recognized valor through the issuance of temporary, honorary brevet ranks. The notoriously difficult Scott was also involved in a row over brevet ranking, which led one antebellum observer of the military to declare, "The annals of the army show more disputes to have arisen in consequence of this brevet rank than all other matters in dispute. It seems to have had the property of transmuting the calmest and best-tempered men into hectoring and quarrelsome Bobadils." While Scott only was promoted to brevet lieutenant general, Grant, during the Civil War, achieved the full-fledged Regular Army rank of lieutenant general, the first officer to hold that rank since George Washington.

The highest Confederate rank was full general. During the summer of 1861, Confederate president Jefferson Davis was authorized by Congress to appoint five men to the rank, in order of seniority—with predictable results. Joseph E. Johnston, a hero of the First Battle of Manassas (1861) and the Regular Army's highest-ranking officer to have resigned and joined the Confederacy, was only fourth on the list and accused the president of having "tarnished my fair fame as a soldier and a man." The two feuded for the rest of the war.