The Branch Church was formed as a Congregational Church on December 29, 1803. The first pastor was Reverend Joshua Spalding. Pews and seats were sold to the public and an annual assessment on these was made to support pastors. On April 26, 1815, the church joined the Londonderry Presbytery, and on June 5, 1824 petitioned the General Court to change the name from "Branch Church" to "First Presbyterian Church in Salem." A request was made to the selectmen on June 4, 1828 to change the name of the street where the church was located from "Branch Street" to "Howard Street" and on June 11, 1828, a petition was made to the Commonwealth of Massachusetts to change the name of the church from "Frist Presbyterian Church in Salem" to "Howard Street Church."

The Church experienced financial difficulties throughout its history and a succession of pastors came and went who had trouble collecting their salaries. In 1848, some of the proprietors petitioned to sell the property and to divide the proceeds among the proprietors, but apparently this did not come to pass since the church still existed in 1867. The last minister, Reverend Charles C. Beaman, resigned on October 2, 1864. The church struggled along for a few more years, but with the effects of the Civil War, no serious attempt was made to continue operations of the society. The property was sold at auction on June 28, 1867 and a school was constructed on the site. The Howard Street Church bell was given in trust to the Mayor of Salem as an alarm and was moved to the belfry of the Central Baptist meeting house on St. Peter's Street. Sale of the property amounted to $3,825.34, and after payment to creditors, nothing was left for the proprietors. A closing history of the church, written by Rev. Charles C. Beaman appears in the Essex Institute Historical Collections, volume 11, January 1872, pages 241-248.