In 1754 the Oneida chief Monacatoocha (Scarouady) led about 200 pro-British Native Americans (Iroquois, Lenape, and Shawnee) from their village of Logstown on the western frontier, to take refuge at George Croghan's trading post.

Following General Edward Braddock's defeat in July 1755, Governor Robert Hunter Morris ordered it renamed Fort Shirley and had several other forts built in a defensive line, to protect settlers from Native American attacks.

[8]: 310  The narrow gauge East Broad Top Railroad (EBT) was constructed through Shirleysburg in 1873.

The Benjamin B. Leas House was listed on the National Register of Historic Places in 1984.

According to the United States Census Bureau, Shirleysburg has a total area of 0.4 square kilometres (0.2 sq mi), all land.

[4] The western border of the borough follows Aughwick Creek, a northward-flowing tributary of the Juniata River.