St. John's began with occasional services in the home of Judge Ross (on the hill above the present church) led by a priest from Keeseville in 1849. Incorporated in 1853 as part of the diocese of New York, the congregation moved into its present building in 1881. The church was the remodeled private school house built by Judge Ross in 1835. It had been built with the idea it would eventually become an Episcopal church. The rectory was built next door about the same time. Persell Hall was added in 1984. St. John's established missions in Boquet (1853), in Elizabethtown as the present Church of the Good Shepherd (1882 ), and in Willsboro as St. Mary's (1902) with the church in Elizabethtown continuing its ministry today. Regionally, St. John's works closely with all the local churches and is part of the Episcopal Northern Adirondack Deanery.

Although occasional Episcopal services were held in Essex as early as 1800, it was not until 1849, when Essex' population had risen to over 2,000, that there was worship here on a regular basis. Beginning that year, The Rev. Fernando Cortes Putnam, missionary priest to Keeseville and Essex, led services in Essex on alternate Sundays, traveling between the towns over Willsboro Mountain by stage-coach.

During these early years missionaries were encouraged to visit Hickory Hill, the home of Judge Henry H. and Susannah Ross (which still stands just above St. John's). Services often were held there or in the private schoolhouse erected by Judge Ross before 1835 for the use of his children and friends. The schoolhouse, now the worship space of St. John's Church, was designed and built with the idea that it would eventually function as a worship space.
St. John's Church was formally incorporated at a meeting in the basement of the Essex Baptist meeting house on March 21, 1853. St. John's established a mission in nearby Boquet in the same year. Later, missions were established in Elizabethtown (1882) and Willsboro (1902).

The Ross' schoolhouse began to be used as a church during or shortly before the year 1854. In the 1870's efforts were directed to erecting a new building, but the idea of remodeling the schoolhouse triumphed.

During the rectorship of the Rev. Eugene L. Toy (1878-1883) the school was moved a short distance to its current location and remodeled to designs by a former rector, the Rev. John Henry Hopkins, Jr., who also designed and donated the marble altar attached to the South wall. At the same time, the rectory was built on the east half of the lot. (You may be familiar with Mr. Hopkins as the author of the well-known Christmas carol "We Three Kings.")
On June 29, 1881, the Rt. Rev. William Crosswell Doane, first bishop of the diocese of Albany, consecrated St. John's Church. At the time, St. John's had 90 communicants.

St. John's congregation, like the population of Essex itself, shrank in the closing years of the nineteenth century. However, the Crater Club , a summer colony just south of Essex, became popular with Episcopalians, and for many years bolstered St. John's summer congregation.

During the first half of the 20th century, St. John's was served by seasonal rectors, usually May through September, with supply clergy or lay readers leading services in other months.
In 1952, the Rev. Albert Anderson began a year-round joint rectorship of St. John's and Good Shepherd in Elizabethtown. This "yoked" arrangement continued under The Rev. David Langdon and other rectors until 1994.

Through 1983 rectors lived in Elizabethtown, and clergy had no ongoing pastoral presence in Essex. The practice of having "summer rectors," sometimes drawn from clergy residents of the Crater Club, continued at St. John's until the rectorship of the Rev. A. William Cooper, Jr. (1982-1994). The Cooper family moved into the rectory in Essex, the first time the house had been so used for many years.
During the 1970's and continuing under the rectorship of Fr. Cooper, St. John's expanded its ministry through establishment of an endowment fund and the addition of a space for meetings, education, and other church functions. This hall, dedicated to the Rt. Rev. Charles B. Persell, Jr., Suffragan Bishop of Albany, was completed in 1984. In 1987 a garden and columbarium area behind the hall was dedicated to the late Rt. Rev. Robert B. Hall, 11th Bishop of Virginia, another long-time friend and summer member of St. John's.

During the rectorship of Fr. Cooper, St. John's began the process of liturgical renewal reflected in the 1979 revision of the Book of Common Prayer: Eucharist (Holy Communion) became the primary service on all Sundays; and a freestanding altar table was procured so that the presider could face the people. Fr. Cooper also instituted St. John's locally famous weekly potluck suppers.

In 1994 St. John's made the bold decision to seek its own resident rector, someone who could concentrate energies in the lakeshore region we have defined as our area of mission. Under the guidance of interim priest Wayne Schwab, former Evangelism Officer of The Episcopal Church, St. John's began focusing on the ministries of the baptized, lay as well as ordained. A thriving Sunday School for children was established, and the congregation of year-round residents was strengthened.

In June 1996 St. John's called its first full-time rector in nearly 85 years, The Rev. Glen Michaels.  Under Fr. Glen's leadership, with the assistance of Fr. Wayne Schwab, St. John's has been at the forefront of efforts within the Episcopal Church to form laity as "missionaries of Jesus Christ in every arena of daily living".

In the Spring of 1999 the front entries to St. John's were redone by local stone masons Al Ulmer and Terry Dinnon. Working from the conceptual design of architect Van Schwab, they used Essex limestone and Ausable Forks granite to create a plaza and entries that are fully handicapped accessible yet fit the historic character of our building.

In July 2000, The Rev. George H. Easter became Priest-in-Charge as the congregation began the search for a new rector after Fr. Michaels left.  The Rev. A. Wayne Schwab again took over as Interim Priest until the search ended in July 2002, when The Rev. Eileen E. Weglarz, St. John's first woman member of the clergy, accepted a call to be Vicar.  Mother Eileen Weglarz resides in the Rectory next to the Church.