After graduating from the United States Military Academy at West Point in 1855, Comstock served with the Army Corps of Engineers.

[2] After the close of the war, Comstock served on the military commission for the trial of the conspirators in the assassination of President Abraham Lincoln.

[2] At the commencement of the Civil War, Comstock, then holding the rank of first lieutenant in the Regular Army, was transferred from West Point to Washington, D.C.

[4] When the Army of the Potomac took the field in the spring of 1862 during Maj. Gen. George B. McClellan's Peninsular Campaign, Comstock continued to serve as Barnard's assistant.

During the Fredericksburg Campaign, Comstock was faced with the difficult task of constructing pontoon bridges over the Rappahannock River, a debacle which proved to be one of the most challenging of his career.

[4] Due to confusion in Washington, D.C. at the War Department, the materials necessary for the construction of the bridges did not arrive at Falmouth, Virginia at the same time as the Army of the Potomac.

[5] When the material for the bridges finally did arrive, Comstock personally led men from the 50th New York Engineers in seeing to the task of construction.

In that capacity, he played an important role in the Battle of Chancellorsville, overseeing the construction of pontoon bridges over various rivers which first allowed the advance of the Army of the Potomac and later facilitated its retreat after Union forces were defeated.

[4] After the Battle of Chancellorsville, Comstock was transferred to the Army of the Tennessee which was, at that time, involved in the Siege of Vicksburg, Mississippi, under the command of Maj. Gen. Ulysses Grant.

This victory marked a major turning point in the war as the Union Army gained control of the Mississippi River.

Grant determined to command in the field, following and directing the movements of the Army of the Potomac in a major offensive during the summer of 1864 known as the Overland Campaign.

[4] His efforts were particularly successful during the Battle of the Wilderness for which Comstock won a commendation from Grant and a brevet promotion to lieutenant colonel in the Regular Army.

Volunteers, to rank from January 15, 1865, for gallant services in the capture of Fort Fisher[7] and the U.S. Senate confirmed the award on February 14, 1865.

[4] In March 1865, Grant again dispatched Comstock to aid in a key siege operation—this time to Mobile, Alabama, the last Confederate stronghold on the Gulf of Mexico.

While Comstock was serving in Alabama, Gen. Robert E. Lee surrendered to Grant after the Battle of Appomattox Courthouse, essentially ending the Civil War.