He served in the Union Army during the American Civil War, participating in the Battle of Fort Donelson, Battle of Shiloh, and Battle of Monocacy as well as managing operations for the Union Army in Indiana in July 1863 when Confederate general John Hunt Morgan invaded the state during Morgan's Raid.
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After the Battle of Monocacy on July 9, 1864, Colonel Gilmor's command, along with Brig. Gen. Bradley T. Johnson's infantry, made a series of raids around Baltimore going as far east as Magnolia Station in Harford County, Maryland and Fork, Maryland.
The victory cleared the way for Early’s entry into Maryland as part of the third and last Confederate invasion of the North, culminating in a Pyrrhic victory at Monocacy Junction near Frederick, Maryland on July 8.