The congregation of Saint John's Church - part of the Episcopal (or, Anglican) Church - has worshiped together on the same site since 1843. At that time the area now known as the Waverly and Charles Villages - the neighborhood in northeastern Baltimore city ministered to by Saint John's Church - was actually the small village of Huntingdon, Maryland, a collection of about seventeen great estates and houses, and the more modest homes of a new and emerging middle class. (The estate names of Huntingdon are synonymous with old Baltimore: Montebello, Clover Hill, Homewood, Guilford, Greenmount, and Homestead.)

The village, which extended from Huntingdon Avenue (in the present day neighborhood of Remington) on the West to the Harford Road on the east; from Huntingdon Avenue (now 25th Street) on the south to Boundary Avenue (42nd Street) in the north, was annexed to Baltimore City in 1888 and the post office was renamed Waverly, after Sir Walter Scott's 'Waverley' novels. Charles Village was created out of this area approximately one decade later.

In November 1843 the Reverend W. A. Hewitt was sent to the village of Huntingdon by Bishop Whittingham at the request of one Mr Thomas Hart who wished to have some of his grandchildren baptized without making the journey to the parish church, Saint Paul's, in Baltimore. The bishop was eager to establish new congregations in Maryland which would embody the ideals of the "Oxford Movement," (which evolved from the Tractarian Movement) a spiritual renewal movement making itself strongly felt throughout the Anglican Church in England and elsewhere. Saint John's Church was born with those baptisms and that spiritual renewal.

The first services were held in an old revolutionary war barracks located some thirty yards southwest of the present church building; on 10 July 1844, Saint John's Church was legally incorporated as a diocesan mission church within the bounds of Saint Paul's parish and by 1845 it was an independent congregation. The congregation laid the cornerstone for its first church in April of 1846 and saw its consecration by Bishop Whittingham on 11 November 1847 and it was determined that the church should be a "free" church - there were to be no pew rents, ever.

For the first two years the rector returned his stipend to the treasurer as his offering toward the building expenses (he also installed the furnace at his own expense, assuring the warm devotion and gratitude of his flock). However, in 15 May 1858, just eleven years after its consecration this lovely new building was gutted by fire and burned to the ground.

The congregation was poorer, but undaunted, and the cornerstone of a new building, the present church, was laid on 11 September 1858 by their faithful father in God, Bishop Whittingham. The first service in this building was held on 22 May 1859, and its consecration was on All Saints' Day, 1 November 1860. The congregation prospered, as did its parishioners, and a Parish House (1866) and a Rectory (1868) were added, all in matching 'gothick' style.

The church, and for the most part the other buildings, were built according to the principles of the Cambridge, England, Ecclesiological Society which devoted itself to the revival of the 'gothick style' in architecture, and all the appurtenances appropriate to the style and dignity of that setting. The Oxford Movement brought with it a matching revival of dignity and ceremonial in the worship of the church and the interior decoration reflected this.

The original church on this site, patterned after Saint Michael's, Long Stanton, in England, was a pure example of English 'country gothick' and this design involved a long nave, lancet windows, thick low medieval walls, and a high, steep-pitched roof. There was a south porch and relatively small sanctuary at the east end.

The present building preserved most of those features, and was enlarged in 1875 adding transepts (to create the classic cruciform shape evident today), a baptistery (the present Lady Chapel), sacristy, enlarged sanctuary, and a rather glorious bell tower and spire. The interior decoration was finally completed in 1895 in the same Victorian gothic revival style.

After several "modernizations" of the decor, neglect, and eventual whitewash(!), the restoration of much of the original decoration was begun in 1983-85 by the Reverend R. Douglas Pitt, the eleventh rector. This work was resumed in 1994 under the Reverend Jesse L. A. Parker, twelfth rector, and continues as of this writing. All of the restoration work has been accomplished by the well-known decorative artist Janet Pope, of J. Pope Studios, Baltimore, which specializes in historic decorative restoration.

In June 2016, after serving this parish for 25 years as rector, the Reverend Parker retired. In September of that year, we welcomed the Reverend Jeffrey Charles Hual as our Priest-in-Charge. "Father Jeff," as he is known, came to us following a curacy at Saint Paul's Parish, K Street, in Washington, D.C. The parishioners of Saint John's are quite proud of our long history of serving Our Lord through ministry and worship, and we look forward to continuing these efforts for many years to come, as well as finding new opportunities for ministry in the city of Baltimore and the world.