Gen. George McClellan used the Pry House as the headquarters for the Union Army of the Potomac. Officers brought some of the Pry furniture out on the lawn. There eyewitnesses described a "small redan built of fence rails" with telescopes mounted, and how the commander "stood in a soldierly attitude intently watching the battle." Reporter Charles Coffin rode to "the large square mansion of Mr. Pry" where "the general was sitting in an arm chair.. his staff were about him, their horses saddled and bridled, were hitched to the trees and fences." When President Lincoln visited in October, Gen. McClellan brought him to the Pry house to see the former headquarters site.
Positioned on high ground, using flags or torches waving back and forth to "talk" to each other, both armies used this new signal technology that permitted rapid communication across the battlefield. Two of their most important signal stations were here at the Pry House (headquarters station) and on Elk Ridge (mountain station), the high ground over a mile to the east. The Manual of Signals stated that with a 12-foot staff and 4-foot flag, signals "are easily read at a distance of 8 miles."
After the battle, the Antietam Valley was described as "one vast hospital." With more than 18,000 soldiers wounded in the two armies, over one hundred field hospitals were established in houses, barns, churches, and tents. Some operated briefly; others housed the sick and suffering for months. The Pry family home and barn were used to care for the wounded, primarily from the Union Second Corps. Gen. Joseph Hooker was brought to the house briefly after being wounded near the Cornfield before being transferred to Washington, D.C.