Saint John the Evangelist Church was founded in 1875, when members of the Saint Stephen's Guild of Trinity Church, Newport, decided to start a mission in the Point section of Newport. They were encouraged in this effort by Trinity's rector, the Reverend Doctor I. P. White. At the time, the Point had no other house of worship.

The new mission held its first service on Sunday, July 11, 1875, in rooms on the corner of Poplar and Third Street that were provided by Peter Quire. In a short time, the mission outgrew these rooms and raised money to build a chapel to accommodate 250 worshipers. The first service in the board-and-batten Gothic Revival building was celebrated on February 13, 1876. Today this building serves as S. John's Guild Hall.

From its earliest days, S. John's offered traditional Anglican worship to persons of all races. It was the first Episcopal church on Aquidneck Island to celebrate the Eucharist every Sunday, and its founders included several African-Americans.

The Free Chapel of Saint John the Evangelist remained a mission of Trinity Church with services conducted by its rector or its curate or a guest clergyman until September 1882, when it became an independent parish within the Episcopal Diocese of Rhode Island. The following year, the church reported to the diocese that it had 100 members, most of whom had transferred from Trinity. The next six years were a period of financial peril for the small congregation. In 1889, the vestry decided reluctantly to reattach the church as a mission of Trinity Church; S. John's rector, the Reverend S. Wilson Moran, who had worked most diligently to make the parish solvent, retired.

Only two years later, S. John's was able to become independent again, thanks to the generosity of Sarah Titus Zabriskie. Miss Zabriskie was a wealthy, socially prominent divorce' who let it be known that she planned to support the church. In 1891, the vestry rescinded its earlier decision and voted to reestablish S. John's as an independent parish. The following year, Miss Zabriskie inherited a vast sum from her mother, Sarah Jane Titus Zabriskie, and began to fulfill her pledge to S. John. She funded the construction of a new sanctuary to be built of brownstone in the style of an English parish church of the 13th century a most appropriate choice for a congregation interested in reviving the Anglo-Catholic liturgy of that period. In November 1894, the Zabriskie Memorial Church of Saint John the Evangelist was completed at a cost of $100,000 and consecrated. Meanwhile, the former chapel building was deconsecrated and remodeled extensively at the parish's expense to serve as the its parish hall. Only two years after these efforts, the church's rector, Father Buckey, resigned and S. John's vestry spent months searching for a replacement. In 1897, the vestry called the Reverend Charles Frederick Beattie to serve as rector. He guided the church through a period of peace until his death in 1919. His tenure saw the addition of many beautiful accessories to the church, most notably the chapel in the south transept of the sanctuary, the Italian creche, and the Belgian Stations of the Cross. In his memory, a handsome rood screen was added to the interior of the church done in harmony with the chapel carving.

Under the guidance of the next rector, Father Julian Delamater Hamlin, S.John's acquired the two properties on Poplar Street from the Guild Hall to Washington Street. The church used the 18th century Dennis House as its rectory and the Greek Revival Crandall House, built in 1832, for parish activities.

In 1929, Father Hamlin accepted a call to the Church of the Advent in Boston and left S. John's in the hands of Dean Charles S. Hutchinson. Father Hutchinson's first duty was to cope with the stock market crash, which all but annulled the church's endowment fund. With the aid of the senior warden, Admiral Reginald R. Belknap, the church was able to survive this calamity.

By 1941, Father Hutchinson's health was failing, so he resigned, and the vestry called the Reverend Arthur H. Austin as his replacement. Father Austin inaugurated many repairs to the buildings. In addition to repairs to the Guild Hall and Rectory, the church's missing roof tiles were replaced with copper roofing, the east wall was repaired, and many of the leaded windows were mended. These tasks were undertaken before war shortages made further work impossible.