Unfortunately the early records of the Sunbury Presbyterian Church are no longer in existence. A flood in early 1867 had swept away the bridge across the Susquehanna River. The Sunbury Elders, traveling to the Presbytery Meeting in Lewisburg in April, had to make the passage by boat. By a sudden movement of the boat the record book was torn from hands of one of the Elders, it fell into the water and was swept down stream.

All that is known of the early history of the church has been gleaned from other sources. In 1770, the Synod of Pennsylvania and New York appointed Elders to do missionary work in the frontier settlements, among the Indians and at Fort Augusta. Sunbury called its first minister in 1787, however it can be assumed that the church was founded at least two years earlier, in 1785. The first minister called to serve the Sunbury church was the Reverend Hugh Morrison, a licentiate of the Presbytery of Root in Ireland, who served until 1804. The two longest serving ministers were the Reverend Chester W. Todd, S.T.D. who served twenty-five years, from 1919 to 1944, and the Reverend Charles B. Almond who served twenty-four years, from 1945 to 1969.

The congregation first worshipped with the German Reformed congregation in a log church at Second and Chestnut Streets. The first "wholly Presbyterian" church was a small one-story brick building erected on a lot purchased on the northeast corner of Chestnut and Third Streets. In 1870 a new church was built on the present site Market Street with an impressive 130’ spire. The spire was condemned in 1926 and brick towers on each corner of the building soon graced the building. In 1939 the towers were remodeled to their present form. A fire in 1911 ruined the organ, finish of the woodwork, and the windows that had been installed in 1909. The first floor sustained water damage. Fortunately the pews were not destroyed and have continued to serve the congregation from 1870 to this day.

The cornerstone for the Sunday School building was laid in 1921 with dedication of the new addition occurring on June 11, 1922. Since that time the church and Sunday School building have been renovated and remodeled several times, the most extensive renovation occurring in 1972 which included the construction of the Almond Chapel in memory of the Reverend Charles B. Almond and the Becker Lounge in memory of Anna Louise Becker. In 2005, air conditioning was installed in the sanctuary.

The church has sponsored Scout Troops for many years. Boy Scout Troop No. 307 has been in existence continuously in the church since 1925. There is also a Cub Pack No. 3307. The church also chartered the land known as Camp Hallowing Run outside of Sunbury for the Boy Scouts. In 2003 a Junior Girl Scout Troop was formed in the church.