William Tennent helped found Deep Run Presbyterian Church in Perkasie, Bucks County, Pennsylvania, in 1725. Sources indicate that Deep Run was reported to the Presbytery of Philadelphia in 1732 as the Reverend Tennent's Upper Congregation. Tennent and his successor, Francis McHenry, served both Deep Run and Neshaminy Presbyterian churches until McHenry was formally installed at Deep Run in 1743.

In 1804, Uriah DuBois, pastor of the Deep Run church, began preaching services in the village schoolhouse in Doylestown, and in 1815, a new church building was dedicated at Doylestown. Until 1957, the two congregations were listed together in presbytery records as Deep Run and Doylestown. Note that Deep Run kept no session minutes, membership rolls, or baptism records until 1823. There are also no graveyard records for the cemetery at Deep Run. Through much of the nineteenth century and first half of the twentieth century, worship at Deep Run was limited to an annual service required to maintain ownership of the property.

In 1913, a committee appointed by Philadelphia North Presbytery to examine both the ecclesiastical relationship of Deep Run to Doylestown and the financial condition of Deep Run reported its findings. The committee advised presbytery that in its opinion the Deep Run and Doylestown churches were one ecclesiastical body but two corporations, each incorporated separately. In 1957, the Presbytery of Philadelphia reorganized a separate Presbyterian Church of Deep Run in the old meeting house on Elephant Road in Dublin, Pa., and as of 2009, the two congregations maintain their separate identities.