St. Paul's was established out of the work of the Reverend Charles J.S. Mayo, associate rector at St. John's in Hampton in 1880, who was assigned the renewal of the Episcopal Church in what is now Newport News. In 1881, Mayo began holding interdenominational worship services in a railroad workers' dormitory. On Easter Monday in 1883, Episcopal members of that church formally organized St. Paul's and elected its first vestry.
St. Paul's parish house served as a center for armed forces personnel during World War I. During World War II, it was again used as a canteen for troops leaving from and returning to Newport News. A wing, including a new kitchen and library, was added for the operation of a community Hospitality House program. About 16,000 military personnel made use of the Hospitality House each month.
St. Paul's helped establish other Episcopal Churches in Newport News, including St. Augustine's in 1897, and St. Andrew's in 1919.
St. Paul's has remained in downtown Newport News, despite the significant changes to that area over the past few decades. The area is now dominated by Huntington Ingalls Industries - Newport News Shipbuilding, which employs one of the largest work forces in Virginia. Downtown residents moved out, and other churches closed their doors or relocated. St. Paul's chose to remain to serve the poor, the homeless, and the few neighbors who remained.
St. Paul's partnered with other churches, civic organizations, and individuals to address hunger and poverty in Newport News through the formation of the Community Action Network. It combined traditional ministries, such as feeding programs, clothing and laundry, with counseling, job training, transportation, financial counseling, and employment services, seeking to empower those in need to lift themselves out of poverty. Dwindling resources caused St. Paul's to consider scaling back some of these services, but they decided to continue due to the high level of need. Much of the church's budget went to the Community Action Network.