Prior to the arrival of European settlers, the area in what would become East Berlin was inhabited by the Susquehannock Native Americans.

As early as 1734, German, Irish, Dutch, and Quaker settlers began occupying land in what would later become Adams County.

[4] Following the 1736 signing of a treaty in Philadelphia between Thomas Penn and members of the Six Nations, many settlers began safely moving to the area.

For much of its early history, East Berlin was not legally a borough with its own municipal government, but a part of neighboring Hamilton Township; on November 10, 1879, after town residents petitioned the Court of Adams County, 407 acres of land around the community were officially designated as the borough of East Berlin.

Congressman and abolitionist Thaddeus Stevens briefly owned property in East Berlin from 1832 to 1848 before moving to Lancaster.

Other folklore suggests that an unidentified man in the second story of the tavern on King Street shot at the Confederates as they passed through town, and that two families with the name Lincoln from nearby Dover hid in East Berlin after hearing that Confederates would kill anyone they met named "Lincoln.

"[4] Early himself spent the night at the Zinn farmhouse (named after the woman who owned it) just west of the town on June 27, where he was treated to a variety of Pennsylvania Dutch dishes.

In the 1950s, the East Berlin Municipal Authority was created, which began to construct a sewage and water treatment facility.

[4] In 1967, Kennan had his daughter Grace house Svetlana Stalin, the daughter of Joseph Stalin, in their home in East Berlin following her defection to the United States, where she stayed for the summer; Grace admits that the people of East Berlin did not "know they had a mysterious visitor in their midst.

[8] According to the United States Census Bureau, the borough has a total area of 0.7 square miles (1.8 km2), all land.