Hanover Junction played a large part in the Civil War. During the Battle of Gettysburg in 1863, both soldiers and supplies were transferred from the Northern Central Railroad to the Hanover Branch Railroad at Hanover Junction to complete the journey to Gettysburg. Wounded soldiers were evacuated from the battlefields by rail to hospitals in both Harrisburg and Baltimore. The Northern Central was a target of the Confederate forces during the summer of 1863, with the railroad bridge over the Codorus Creek in Hanover Junction being destroyed, along with the turntable located in the yard. When rail service diminished in the latter half of the 20th century, the depot area of the town was abandoned. However, in 2003, the depot was fully restored and opened as a museum. Ten years later, trains started stopping again at Hanover Junction as Northern Central Railroad began regular operations.