Hanover Junction was an important railroad intersection linking the Northern Central and Hanover-Gettysburg railroads. During the Civil War it was a vital communications and military supply depot. The Confederates targeted Hanover Junction due to both its railroad and telegraph connections.

More than 200 men from the 35th Battalion, Virginia Cavalry commanded by Colonel Elijah White reached Hanover Junction on June 27, 1863. They encountered two companies of the 20th PA Volunteer Militia and drove them back to their lines on a hill overlooking the Codorus Creek Valley. White and his men then headed for the Howard Tunnel while the soldiers of the 20th PA retreated to Wrightsville. The Confederates cut telegraph lines and destroyed railroad bridges and track disrupting communications between Harrisburg and Washington, D.C., and prevented the Union Army from using this railroad system for resupply. By the time the Confederates finished, they had destroyed 19 bridges on the Northern Central Railroad between Harrisburg and Hanover Junction, and three between Gettysburg and Hanover Junction. After the Battle of Gettysburg the bridges were quickly repaired. Approximately 15,580 wounded soldiers were transported from the battlefield to here, and then on to distant hospitals. President Abraham Lincoln changed railroads here, on his way to and from delivering his Gettysburg Address.

The John Scott Hotel now a private home