Brewerton saw his first combat with Battery K during the Peninsular Campaign (March to June 1862), which was the first large-scale offensive carried out by the Union Army in the East. General George McClellan planned to capture Richmond, Virginia by moving his entire Army of the Potomac from the vicinity of Washington, D.C. to Fortress Monroe and attacking from the South. Brewerton and Battery K participated in the sieges of Yorktown (late April) and Williamsburg (early May), and commanded a section of the battery at the Battle of Seven Pines (31 May).
In early June, Henry Brewerton received a transfer to Battery C, 3rd U.S. Artillery. He and his new battery participated in the Seven Days Battles near Richmond, Virginia (25 June to 1 July), which were the culminating actions of the Peninsular Campaign. Henry fought in battles at Mechanicsville (26 June), Gaines' Mill (27 June), White Oak Swamp (30 June), and Malvern Hill (1 July). Although the Peninsular Campaign was a loss for the Federal Army, units such as the batteries Henry Brewerton fought with delivered solid service and received the praise of their commanding officers.
Brewerton received a promotion to 1st Lieutenant after the Peninsular Campaign and was transferred to Battery E of the 5th U.S. Artillery. In December 1863 he received another transfer to the Department of Susquehanna where he served with the department's recruiting office.
Military authorities assigned Henry Brewerton to field service once again in July 1864. He took over command of Battery B, 5th U.S. Artillery from Henry A. du Pont, who had been promoted to command the Artillery Brigade in General George Crook's Army of West Virginia. Brewerton fought with Battery B in the Battles of Opequan (19 September) and Fisher's Hill (22 September), both in Virginia.