When a schism developed in the Presbyterian Church in America in the early-mid 18th century, some members of the Forks of the Brandywine Presbyterian Church withdrew from the congregation and placed themselves under the direction of the Synod of New Brunswick in the early 1740s; they became known as the "New Side" Presbytery. When they built their Meeting House across the Horseshoe Pike, below the old Forks of the Brandywine Church in ca. 1744, they set apart a portion of the land which they had obtained for use as a burial ground. Among those first interred in this graveyard was their pastor, the Reverend William Dean.

This smaller New Side graveyard, which occupies a rectangular space of about half an acre, was enclosed by a stone wall in 1796. It has remained without any enlargement, except a small extension on the Southern side in 1860, when the wall was also repaired and capped with flagstone.

In 1822 an iron gate and marble posts at the entrance were placed there, in accordance with the will of Isaac Smith, who also left a small sum for the purpose of keeping the yard and its surroundings in a proper condition. His initials and the year the gate was erected appear engraved on the marble posts flanking the entrance, which have led to some calling this the "Forks of the Brandywine I.S. 1822 Cemetery," though it was originally laid out many decades before then.

After the Old and New Sides reunited in 1758, the New Side meetinghouse and burial ground became property of the united congregation. It, together with the land previously obtained, still remains in the possession of the Forks of the Brandywine Presbyterian Church.

This cemetery should not be confused with the Lower Brandywine Presbyterian Church Cemetery just over the Pennsylvania/Delaware border, south of Kennett Square.