The First Presbyterian Church of Philadelphia was organized around 1692. Religious services began in a building known as the "Barbadoes Warehouse," located on the northwest corner of Second and Chestnut Streets. For a time, both Baptists and Congregationalists shared this facility with the Presbyterians.

In 1704, the congregation moved to the south side of High Street (now Market Street) at the corner of Bank Street. Here the first Presbyterian church in Philadelphia was established. The church later became known as "Old Buttonwood." In 1729, the structure underwent enlargement with some assistance from Boston contributors. Then in 1793, it was renovated and made more spacious and elegant. Twenty-seven years later it was abandoned, due to unsafe conditions and the encroachment of the surrounding business district.

The burial ground adjoining the church was finally closed in 1847. In 1848, the First Presbyterian Church reinterred 900 of the bodies that were removed from Bank Street in the burial lot next to Third Presbyterian Church. Families that opted to have their ancestors reinterred in a vault at Laurel Hill Cemetery were not allowed to bring the headstones with them; these were propped up against the walls down at "Old Pine."

When the Presbyterian Historical Society started looking for a new home in the 1960s, it purchased a vacant lot adjoining the Third Presbyterian church and burial ground. As construction began, the old south wall of the church cemetery was torn down. To preserve the 43 tombstones, the architects decided to embed thirty of them in the northern wall of the new building. The remaining 13 were propped against the western wall of the Old Pine burial ground, where they remain to this day.